Publications: PROF David Baker

Yang H, Lin D-Z, Li Z, Yan Y, Zhao Z-H, Lee B, Song CW, Wang S et al. ( 2026 ) . Programmed synthesis of mesoporous protein crystals in cellular reactors . Nature Nanotechnology1 - 9 .

Wang S, Xie Y, Chmielewski D, Weidle C, Shu T, Ahn G, Kibler RD, Hernandez C et al. ( 2026 ) . Author Correction: De novo design of quasisymmetric two-component protein cages . Nature1 - 1 .

Liu Y, Arús BA, Mishra K, Wang T, Zhang K, Luciano MP, Bandi VG, Kumar A et al. ( 2026 ) . De Novo Design of Near-Infrared Fluorescence-Activating Proteins . Journal of the American Chemical Society

Xu Y, Li Y, Zheng H, Delfosse ES, Gao Y, Baker D, Ji P ( 2026 ) . De Novo Design of Miniature and Efficient Metallo-Ketoreductases . Journal of the American Chemical Society vol. 148 , ( 21 ) 21518 - 21529 .

Wang S, Xie Y, Chemielewski D, Weidle C, Shu T, Ahn G, Kibler RD, Hernandez C et al. ( 2026 ) . De novo design of quasisymmetric two-component protein cages . Nature1 - 8 .

Lee S, Chmielewski D, Wang S, Kibler RD, Shin J, Carr A, Park Y-J, Veesler D et al. ( 2026 ) . Design of one-component quasisymmetric protein nanocages . Nature1 - 7 .

Cabrerizo-Aguado D, Barbugian F, Ginebra M-P, Wang X, Baker D, Manero JM, Guillem-Marti J ( 2026 ) . Antibacterial and cell-instructive chitosan/NeoNectin hydrogels crosslinked via click chemistry enable osteogenic differentiation within ultra-soft matrices . Carbohydrate Polymers vol. 385 ,

Yang W, Wang S, Lee GR, Zhang JZ, Courbet A, Juergens D, Wang X, Schlichthaerle T et al. ( 2026 ) . The past, present and future of de novo protein design . Nature vol. 652 , ( 8112 ) 1139 - 1152 .

Haddox HK, Rocklin GJ, Motta FC, Strickland D, Halabiya SF, Cordray C, Park H, Klavins E et al. ( 2026 ) . Using experimental results of protein design to guide biomolecular energy-function development . PLOS Computational Biology vol. 22 , ( 4 )

Guo Z, Smutok O, Lee GR, Cui Z, Qianzhu H, Kish M, Ergun yva C, Wu K et al. ( 2026 ) . Artificial allosteric protein switches with machine-learning-designed receptors . Nature Biotechnology1 - 11 .

Lee GR, Pellock SJ, Norn C, Tischer D, Dauparas J, Anishchenko I, Mercer JAM, Kang A et al. ( 2026 ) . Small-molecule binding and sensing with a designed protein family . Nature Communications vol. 17 , ( 1 )

Morris E, Lozhkin B, Uhrhan J, Kalvet I, Basler S, Jakob RP, Baker D, Ward TR ( 2026 ) . Design, Optimization and Characterization of a de novo Gold Hydroaminase . ACS Catalysis vol. 16 , ( 7 ) 6387 - 6395 .

Yadav Schmid S, Helfrecht B, Stegmann A, Legg BA, Pyles H, Chen J, Edison JR, Ziatdinov M et al. ( 2026 ) . Impact of solvent forces and broken symmetry on the assembly of designed proteins at a liquid-solid interface . Nature Communications vol. 17 , ( 1 )

Zhang JZ, Li X, Batingana AR, Liu C, Jiang H, Shannon K, Huang BJ, Wu K et al. ( 2026 ) . De novo design of Ras isoform selective binders . Cell Chemical Biology vol. 33 , ( 3 ) 396 - 408.e7 .

Lowe C, Yu LT, Tu J, O’Reilly I, Miura-Stempel E, Larson HC, Bodinger CC, Baker D et al. ( 2026 ) . Nanomolar Sensitivity Chirality Transfer from Designed Helical Repeat Proteins to Achiral CdS Nanorods . Nano Letters vol. 26 , ( 11 ) 3776 - 3783 .

Yan Y, Lu J, Li Z, Zhao Z, Shay TF, Wang S, Lei Y, Wang Y et al. ( 2026 ) . Genetically encoded assembly recorder temporally resolves cellular history . Nature vol. 652 , ( 8111 ) 1049 - 1059 .

Bloom BM, Payne O, Valero-Hernandez E, Kang AS, Singh BK, Baker D, Harris K, Cutino-Moguel T et al. ( 2026 ) . Multiple sclerosis and autoimmunity: learnings from post-streptococcal autoimmunity . Multiple Sclerosis and Related Disorders vol. 109 ,

Giovannoni G, Payne O, Valero-Hernández E, Kang AS, Singh BK, Baker D, Harris K, Cutino-Moguel T et al. ( 2026 ) . Post-streptococcal Autoimmunity and Its Relevance to Epstein–Barr virus as the Potential Cause of Multiple Sclerosis . Journal of Infectious Diseases

Shi C, Shen H, Bae Y, Heo J, Zhang S, Yao L, Baker D, De Yoreo JJ ( 2025 ) . The Anisotropic Adsorption of De Novo Allosteric Two‐Component Protein Fibers on Mica Surfaces . Advanced Functional Materials vol. 36 , ( 23 )

Adeniran AA, Giovannoni G, Baker D, James LK ( 2025 ) . Epstein–Barr virus and spontaneous lymphoblastoid cell lines: establishment, molecular characteristics, immune modulation, and therapeutic insight . Clinical & Experimental Immunology vol. 219 , ( 1 )

Liu B, Greenwood NF, Bonzanini JE, Motmaen A, Meyerberg J, Dao T, Xiang X, Ault R et al. ( 2025 ) . Design of high-specificity binders for peptide–MHC-I complexes . Science vol. 389 , ( 6758 ) 386 - 391 .

Farinas A, Rutledge J, Bot VA, Western D, Ying K, Lawrence KA, Oh HS-H, Yoon S et al. ( 2025 ) . Disruption of the cerebrospinal fluid–plasma protein balance in cognitive impairment and aging . Nature Medicine vol. 31 , ( 8 ) 2578 - 2589 .

Baker D, Alfredsson L, Hedström AK, Schmierer K ( 2025 ) . Mechanistic biology linking traumatic brain injury to multiple sclerosis susceptibility . Journal of Neurology Neurosurgery & Psychiatry vol. 96 , ( 12 ) 1169 - 1174 .

Wang X, Guillem‐Marti J, Kumar S, Lee DS, Cabrerizo‐Aguado D, Werther R, Alamo KAE, Zhao YT et al. ( 2025 ) . De Novo Design of Integrin α5β1 Modulating Proteins to Enhance Biomaterial Properties . Advanced Materials vol. 37 , ( 34 )

Woodward CH, Chaudhuri A, Chen XT, White WL, Garcia KC, Baker D, Sgourakis NG ( 2025 ) . Solution mapping of MHC-I:TCR interactions using a minimalistic protein system . Proceedings of the National Academy of Sciences of the United States of America vol. 122 , ( 24 )

Stordy BP, Sepahi Z, Patrón GD, Yang W, Goodson AD, Blackadar C, Tavares AJ, Lin G et al. ( 2025 ) . The Binding Affinities of Serum Proteins to Nanoparticles . Journal of the American Chemical Society vol. 147 , ( 24 ) 20475 - 20492 .

White WL, Yirdaw HK, Ben-Sasson AJ, Groves JT, Baker D, Kueh HY ( 2025 ) . Proofreading and single-molecule sensitivity in T cell receptor signaling by condensate nucleation . Proceedings of the National Academy of Sciences of the United States of America vol. 122 , ( 22 )

Giovannoni G, James L, Adeniran AA, Gold J, Young LS, Selwood DL, Baker D, Dobson R ( 2025 ) . The case for targeting latent and lytic Epstein-Barr virus infection in multiple sclerosis . Brain vol. 148 , ( 9 ) 3057 - 3071 .

Lee JD, Nguyen A, Gibbs CE, Jin ZR, Wang Y, Moghadasi A, Wait SJ, Choi H et al. ( 2025 ) . Monitoring in real time and far-red imaging of H2O2 dynamics with subcellular resolution . Nature Chemical Biology vol. 22 , ( 4 ) 556 - 567 .

Kshirsagar M, Meller A, Humphreys IR, Sledzieski S, Xu Y, Dodhia R, Horvitz E, Berger B et al. ( 2025 ) . Rapid and accurate prediction of protein homo-oligomer symmetry using Seq2Symm . Nature Communications vol. 16 , ( 1 )

Li Y, Harris BS, Li Z, Shi C, Abdullah J, Majumder S, Berhanu S, Vorobieva AA et al. ( 2024 ) . Water, Solute, and Ion Transport in De Novo-Designed Membrane Protein Channels . ACS Nano vol. 19 , ( 2 ) 2185 - 2195 .

Kibler RD, Lee S, Kennedy MA, Wicky BIM, Lai SM, Kostelic MM, Carr A, Li X et al. ( 2024 ) . Design of pseudosymmetric protein hetero-oligomers . Nature Communications vol. 15 , ( 1 )

Lee S, Kibler RD, Ahn G, Hsia Y, Borst AJ, Philomin A, Kennedy MA, Huang B et al. ( 2024 ) . Four-component protein nanocages designed by programmed symmetry breaking . Nature vol. 638 , ( 8050 ) 546 - 552 .

Dowling QM, Park Y-J, Fries CN, Gerstenmaier NC, Ols S, Yang EC, Wargacki AJ, Dosey A et al. ( 2024 ) . Hierarchical design of pseudosymmetric protein nanocages . Nature vol. 638 , ( 8050 ) 553 - 561 .

Allen-Philbey K, Stephenson S, Doody G, MacDougall A, Aboulwafaali M, Ammoscato F, Andrews M, Gnanapavan S et al. ( 2024 ) . Effects of cladribine on intrathecal and peripheral B and plasma cells . Clinical & Experimental Immunology vol. 219 , ( 1 )

Glögl M, Krishnakumar A, Ragotte RJ, Goreshnik I, Coventry B, Bera AK, Kang A, Joyce E et al. ( 2024 ) . Target-conditioned diffusion generates potent TNFR superfamily antagonists and agonists . Science vol. 386 , ( 6726 ) 1154 - 1161 .

King BR, Sumida KH, Caruso JL, Baker D, Zalatan JG ( 2024 ) . Computational Stabilization of a Non‐Heme Iron Enzyme Enables Efficient Evolution of New Function . Angewandte Chemie International Edition vol. 64 , ( 2 ) e202414705 - e202414705 .

Jin B, Chen Y, Pyles H, Baer MD, Legg BA, Wang Z, Washton NM, Mueller KT et al. ( 2024 ) . Formation, chemical evolution and solidification of the dense liquid phase of calcium (bi)carbonate . Nature Materials vol. 24 , ( 1 ) 125 - 132 .

Ammoscato F, Wafa M, Skonieczna J, Bestwick J, Monero R, Andrews M, De Trane S, Holden D et al. ( 2024 ) . Cladribine tablets in relapsing-remitting multiple sclerosis preferentially target B-cells . Clinical Immunology vol. 269 ,

Huang B, Abedi M, Ahn G, Coventry B, Sappington I, Tang C, Wang R, Schlichthaerle T et al. ( 2024 ) . Designed endocytosis-inducing proteins degrade targets and amplify signals . Nature vol. 638 , ( 8051 ) 796 - 804 .

Humphreys IR, Zhang J, Baek M, Wang Y, Krishnakumar A, Pei J, Anishchenko I, Tower CA et al. ( 2024 ) . Protein interactions in human pathogens revealed through deep learning . Nature Microbiology vol. 9 , ( 10 ) 2642 - 2652 .

Baryshev A, La Fleur A, Groves B, Michel C, Baker D, Ljubetič A, Seelig G ( 2024 ) . Massively parallel measurement of protein–protein interactions by sequencing using MP3-seq . Nature Chemical Biology vol. 20 , ( 11 ) 1514 - 1523 .

Huang B, Coventry B, Borowska MT, Arhontoulis DC, Exposit M, Abedi M, Jude KM, Halabiya SF et al. ( 2024 ) . De novo design of miniprotein antagonists of cytokine storm inducers . Nature Communications vol. 15 , ( 1 )

Sun K, Li S, Zheng B, Zhu Y, Wang T, Liang M, Yao Y, Zhang K et al. ( 2024 ) . Accurate de novo design of heterochiral protein–protein interactions . Cell Research vol. 34 , ( 12 ) 846 - 858 .

Pillai A, Idris A, Philomin A, Weidle C, Skotheim R, Leung PJY, Broerman A, Demakis C et al. ( 2024 ) . De novo design of allosterically switchable protein assemblies . Nature vol. 632 , ( 8026 ) 911 - 920 .

Zhang JZ, Ong S-E, Baker D, Maly DJ ( 2024 ) . Single-cell sensor analyses reveal signaling programs enabling Ras-G12C drug resistance . Nature Chemical Biology vol. 21 , ( 1 ) 47 - 58 .

An L, Said M, Tran L, Majumder S, Goreshnik I, Lee GR, Juergens D, Dauparas J et al. ( 2024 ) . Binding and sensing diverse small molecules using shape-complementary pseudocycles . Science vol. 385 , ( 6706 ) 276 - 282 .

Berhanu S, Majumder S, Müntener T, Whitehouse J, Berner C, Bera AK, Kang A, Liang B et al. ( 2024 ) . Sculpting conducting nanopore size and shape through de novo protein design . Science vol. 385 , ( 6706 ) 282 - 288 .

Peruzzi JA, Gunnels TF, Edelstein HI, Lu P, Baker D, Leonard JN, Kamat NP ( 2024 ) . Enhancing extracellular vesicle cargo loading and functional delivery by engineering protein-lipid interactions . Nature Communications vol. 15 , ( 1 )

Berger S, Seeger F, Yu T-Y, Aydin M, Yang H, Rosenblum D, Guenin-Macé L, Glassman C et al. ( 2024 ) . Preclinical proof of principle for orally delivered Th17 antagonist miniproteins . Cell vol. 187 , ( 16 ) 4305 - 4317.e18 .

Goverde CA, Pacesa M, Goldbach N, Dornfeld LJ, Balbi PEM, Georgeon S, Rosset S, Kapoor S et al. ( 2024 ) . Computational design of soluble and functional membrane protein analogues . Nature vol. 631 , ( 8020 ) 449 - 458 .

Thomson A, Horne R, Chapman C, Bharadia T, Burke P, Colwell E, Harrington M, Boskovic B et al. ( 2024 ) . Engaging a community to focus on upper limb function in people with multiple sclerosis: the ThinkHand campaign case study . Research Involvement and Engagement vol. 10 , ( 1 )

Mistry N, Hobart J, Rog D, Muhlert N, Mathews J ( 2024 ) . Reconciling lesions, relapses and smouldering associated worsening: A unifying model for multiple sclerosis pathogenesis . Multiple Sclerosis and Related Disorders vol. 88 ,

Edman NI, Phal A, Redler RL, Schlichthaerle T, Srivatsan SR, Ehnes DD, Etemadi A, An SJ et al. ( 2024 ) . Modulation of FGF pathway signaling and vascular differentiation using designed oligomeric assemblies . Cell vol. 187 , ( 14 ) 3726 - 3740.e43 .

Ennist NM, Wang S, Kennedy MA, Curti M, Sutherland GA, Vasilev C, Redler RL, Maffeis V et al. ( 2024 ) . De novo design of proteins housing excitonically coupled chlorophyll special pairs . Nature Chemical Biology vol. 20 , ( 7 ) 906 - 915 .

Jiang H, Jude KM, Wu K, Fallas J, Ueda G, Brunette TJ, Hicks DR, Pyles H et al. ( 2024 ) . De novo design of buttressed loops for sculpting protein functions . Nature Chemical Biology vol. 20 , ( 8 ) 974 - 980 .

Yang EC, Divine R, Miranda MC, Borst AJ, Sheffler W, Zhang JZ, Decarreau J, Saragovi A et al. ( 2024 ) . Computational design of non-porous pH-responsive antibody nanoparticles . Nature Structural & Molecular Biology vol. 31 , ( 9 ) 1404 - 1412 .

Craven TW, Nolan MD, Bailey J, Olatunji S, Bann SJ, Bowen K, Ostrovitsa N, Da Costa TM et al. ( 2024 ) . Computational Design of Cyclic Peptide Inhibitors of a Bacterial Membrane Lipoprotein Peptidase . ACS Chemical Biology vol. 19 , ( 5 ) 1125 - 1130 .

Ammoscato F, Skonieczna J, Bestwick J, Holden D, Aboulwafa M, Andrews M, Turner B, Marta M et al. ( 2024 ) . Prospective Longitudinal Study of Cladribine Tablets (CLADB Study) Demonstrates Sustained Reduction in Kappa Free Light Chains in Relapsing Multiple Sclerosis (RRMS) at 96 Weeks (P10-6.008) . Neurology vol. 102 , ( 7_supplement_1 )

de Haas RJ, Brunette N, Goodson A, Dauparas J, Yi SY, Yang EC, Dowling Q, Nguyen H et al. ( 2024 ) . Rapid and automated design of two-component protein nanomaterials using ProteinMPNN . Proceedings of the National Academy of Sciences of the United States of America vol. 121 , ( 13 )

Neunie OAM, Rabbani W, Baker D, Chambers ES, Pfeffer PE, Kang AS ( 2024 ) . Immunogenicity of biologics used in the treatment of asthma . Human Antibodies vol. 32 , ( 3 ) 121 - 128 .

Baker D, Kang AS, Giovannoni G, Schmierer K ( 2023 ) . Neutropenia following immune-depletion, notably CD20 targeting, therapies in multiple sclerosis . Multiple Sclerosis and Related Disorders vol. 82 ,

Allen-Philbey K, De Trane S, MacDougall A, Adams A, Bianchi L, Campion T, Giovannoni G, Gnanapavan S et al. ( 2023 ) . Disease activity 4.5 years after starting cladribine: experience in 264 patients with multiple sclerosis . Therapeutic Advances in Neurological Disorders vol. 16 ,

Santorella E, Balsbaugh JL, Ge S, Saboori P, Pachter JS ( 2023 ) . Proteomic interrogation of the meninges reveals the molecular identities of structural components and regional distinctions along the CNS axis . Fluids and Barriers of the CNS vol. 20 , ( 1 )

Dubuisson N, de Maere d'Aertrijcke O, Marta M, Gnanapavan S, Turner B, Baker D, Schmierer K, Giovannoni G et al. ( 2023 ) . Anaesthetic management of people with multiple sclerosis . Multiple Sclerosis and Related Disorders vol. 80 ,

Seaton A, Baker D, Hedstrom AK, Alfredsson L ( 2023 ) . Organic solvents and Multiple Sclerosis: the doubled risk dilemma . Occupational Medicine vol. 73 , ( 6 ) 300 - 303 .

Nutma E, Fancy N, Weinert M, Tsartsalis S, Marzin MC, Muirhead RCJ, Falk I, Breur M et al. ( 2023 ) . Translocator protein is a marker of activated microglia in rodent models but not human neurodegenerative diseases . Nature Communications vol. 14 , ( 1 )

Zaloum SA, Wood CH, Tank P, Upcott M, Vickaryous N, Anderson V, Baker D, Chance R et al. ( 2023 ) . Risk of COVID-19 in people with multiple sclerosis who are seronegative following vaccination . Multiple Sclerosis Journal vol. 29 , ( 8 ) 979 - 989 .

Pryce G, Sisay S, Giovannoni G ( 2023 ) . Neuroprotection in an Experimental Model of Multiple Sclerosis via Opening of Big Conductance, Calcium-Activated Potassium Channels . Pharmaceuticals vol. 16 , ( 7 )

van Noort JM, Baker D, Kipp M ( 2023 ) . The pathogenesis of multiple sclerosis: a series of unfortunate events . Clinical & Experimental Immunology vol. 214 , ( 1 ) 1 - 17 .

Trippe BL, Yim J, Tischer D, Baker D, Broderick T, Barzilay R, Jaakkola T ( 2023 ) . DIFFUSION PROBABILISTIC MODELING OF PROTEIN BACKBONES IN 3D FOR THE MOTIF-SCAFFOLDING PROBLEM . 11th International Conference on Learning Representations Iclr 2023 .

Baker D, Forte E, Pryce G, Kang AS, James LK, Giovannoni G, Schmierer K ( 2022 ) . The impact of sphingosine-1-phosphate receptor modulators on COVID-19 and SARS-CoV-2 vaccination . Multiple Sclerosis and Related Disorders vol. 69 ,

Vainchtein ID, Alsema AM, Dubbelaar ML, Grit C, Vinet J, van Weering HRJ, Biagini G, Amor S et al. ( 2022 ) . Characterizing microglial gene expression in a model of secondary progressive multiple sclerosis . Glia vol. 71 , ( 3 ) 588 - 601 .

Licht‐Mayer S, Campbell GR, Mehta AR, McGill K, Symonds A, Al‐Azki S, Pryce G, Kipp M et al. ( 2022 ) . Axonal response of mitochondria to demyelination and complex IV activity within demyelinated axons in experimental models of multiple sclerosis . Neuropathology and Applied Neurobiology vol. 49 , ( 1 )

Schmierer K, Redha I, Hammond V, Baker D, Barkhof F, Hooper R, Rashid W, Singh-Curry V et al. ( 2022 ) . 152 AttackMS natalizumab for the treatment of people with inflammatory demyeli- nation suggestive of multiple sclerosis . Journal of Neurology Neurosurgery & Psychiatry . vol. 93 ,

Schmierer K, Baker D, Nawaz T, Allen-Philbey K, Barkhof F, Chataway J, Hooper R, Mihaylova B et al. ( 2022 ) . 153 ChariotMS – cladribine to halt deterioration in people with advanced multiple sclerosis (pwAMS) . Journal of Neurology Neurosurgery & Psychiatry . vol. 93 ,

Allen-Philbey K, Stennett A, Begum T, Johnson AC, MacDougall A, Green S, Dobson R, Giovannoni G et al. ( 2022 ) . Did it hurt? COVID-19 vaccination experience in people with multiple sclerosis . Multiple Sclerosis and Related Disorders vol. 65 ,

Tallantyre EC, Scurr MJ, Vickaryous N, Richards A, Anderson V, Baker D, Chance R, Evangelou N et al. ( 2022 ) . Response to COVID-19 booster vaccinations in seronegative people with multiple sclerosis . Multiple Sclerosis and Related Disorders vol. 64 ,

Baker D, MacDougall A, Kang AS, Schmierer K, Giovannoni G, Dobson R ( 2022 ) . Seroconversion following COVID-19 vaccination: can we optimize protective response in CD20-treated individuals? . Clin Exp Immunol vol. 207 , ( 3 ) 263 - 271 .

Nutma E, Fancy N, Weinert M, Marzin MC, Tsartsalis S, Muirhead RCJ, Falk I, de Bruin J et al. ( 2022 ) . Translocator protein is a marker of activated microglia in rodent models but not human neurodegenerative diseases .

Allen-Philbey K, Marta M, Gnanapavan S, Baker D, Schmierer K ( 2022 ) . Disease activity after cladribine immune reconstitution therapy: To repeat or to retreat? (P9-4.002) . Neurology vol. 98 , ( 18_supplement )

Guo L, Luong V, Gregson A, Baker D, Selwood D ( 2022 ) . VSN16S, an agonist of the cannabinoid receptor, reduces IOP profiles and exhibits neuroprotective properties in a rat model of glaucoma . Acta Ophthalmologica vol. 100 , ( S267 )

Allen-Philbey K, Andrews M, Redha I, Papachatzaki M, Marta M, Gnanapavan S, Mathews J, Turner B et al. ( 2022 ) . CLADRIPLAS: Does cladribine Target CNS plasma cells and reduce neuro-axonal damage in people with MS? . MULTIPLE SCLEROSIS JOURNAL . vol. 28 , 769 - 770 .

Vickaryous N, Rios F, Schalk L, Asardag AN, George K, Kang A, Baker D, Giovannoni G et al. ( 2022 ) . COVID-19 humoral and T-cell mediated vaccination responses in people with multiple sclerosis . MULTIPLE SCLEROSIS JOURNAL . vol. 28 , 680 - 680 .

Upcott M, Tallantyre EC, Scurr MJ, Vickaryous N, Richards A, Anderson V, Baker D, Chance R et al. ( 2022 ) . Humoral and T- cell response to multiple COVID-19 booster vaccinations in people with MS . MULTIPLE SCLEROSIS JOURNAL . vol. 28 , 365 - 366 .

Baker D, Forte E, Pryce G, Kang A, James LK, Giovannoni G, Schmierer K ( 2022 ) . The Impact of Sphinogosine-1-Phosphate Receptor Modulators on COVID-19 and SARS-CoV-2 Vaccination .

Baker D, MacDougall A, Kang AS, Schmierer K, Giovannoni G, Dobson R ( 2021 ) . CD19 B cell repopulation after ocrelizumab, alemtuzumab and cladribine: Implications for SARS-CoV-2 vaccinations in multiple sclerosis . Multiple Sclerosis and Related Disorders vol. 57 ,

Allen-Philbey K, De Trane S, Mao Z, Álvarez-González C, Mathews J, MacDougall A, Stennett A, Zhou X et al. ( 2021 ) . Subcutaneous cladribine to treat multiple sclerosis: experience in 208 patients . Therapeutic Advances in Neurological Disorders vol. 14 ,

Smets I, Holden D, Bianchi L, Ammoscato F, Allen-Philbey K, Baker D, Turner B, Marta M et al. ( 2021 ) . Factors contributing to CSF NfL reduction over time in those starting treatment for multiple sclerosis: An observational study . Multiple Sclerosis and Related Disorders vol. 57 ,

Baker D, MacDougall A, Kang AS, Schmierer K, Giovannoni G, Dobson R ( 2021 ) . Seroconversion following COVID-19 vaccination: Can we optimize protective response in CD20-treated individuals? . Clinical & Experimental Immunology vol. 207 , ( 3 )

Baker D, MacDougall A, Kang AS, Schmierer K, Giovannoni G, Dobson R ( 2021 ) . Seroconversion following COVID-19 vaccination: can we optimize protective response in CD20-treated individuals? . Clinical & Experimental Immunology vol. 207 , ( 3 ) 263 - 271 .

Tallantyre EC, Vickaryous N, Anderson V, Asardag AN, Baker D, Bestwick J, Bramhall K, Chance R et al. ( 2021 ) . COVID‐19 Vaccine Response in People with Multiple Sclerosis . Annals of Neurology vol. 91 , ( 1 ) 89 - 100 .

Rupnik M, Selwood DL ( 2021 ) . Oligodendrocytes, BK channels and the preservation of myelin . F1000Research vol. 10 ,

Baker D, Asardag AN, Quinn OA, Efimov A, Kang AS ( 2021 ) . Anti-drug antibodies to antibody-based therapeutics in multiple sclerosis . Human Antibodies vol. 29 , ( 4 ) 255 - 262 .

Marta M, Baker D, Creeke P, Pryce G, Gnanapavan S, Giovannoni G ( 2021 ) . Antigen-specific tolerization in human autoimmunity: Inhibition of interferon-beta1a anti-drug antibodies in multiple sclerosis: A case report . Multiple Sclerosis and Related Disorders vol. 56 ,

Rupnik M, Baker D, Selwood DL ( 2021 ) . Oligodendrocytes, BK channels and remyelination . F1000Research vol. 10 ,

Giovannoni G, Hawkes CH, Lechner-Scott J, Levy M ( 2021 ) . COVID-19 vaccines and multiple sclerosis disease-modifying therapies . Multiple Sclerosis and Related Disorders vol. 53 ,

Hurley MJ, Deacon RMJ, Chan AWE, Baker D, Selwood DL ( 2021 ) . Reversal of behavioural phenotype by the cannabinoid-like compound VSN16R in fragile X syndrome mice . Brain vol. 145 , ( 1 ) 76 - 82 .

Baker D, Hadjicharalambous C, Giovannoni G ( 2021 ) . Can rheumatologists stop causing demyelinating disease? . Multiple Sclerosis and Related Disorders vol. 53 ,

Allen-Philbey K, Stennett A, Begum T, Johnson A, Dobson R, Giovannoni G, Gnanapavan S, Marta M et al. ( 2021 ) . Experience with the COVID-19 AstraZeneca vaccination in people with multiple sclerosis . Multiple Sclerosis and Related Disorders vol. 52 ,

Allen-Philbey K, De Trane S, Stennett A, Yildiz O, Adams A, Turner B, Marta M, Gnanapavan S et al. ( 2021 ) . Cladribine personalised dosing for active multiple sclerosis: BartsMS cohort follow-up (2528) . Neurology vol. 96 , ( 15_supplement )

Divine R, Dang HV, Ueda G, Fallas JA, Vulovic I, Sheffler W, Saini S, Zhao YT et al. ( 2021 ) . Designed proteins assemble antibodies into modular nanocages . Science vol. 372 , ( 6537 )

Schmierer K, Baker D ( 2021 ) . Highly effective disease-modifying treatment as initial MS therapy . Current Opinion in Neurology vol. 34 , ( 3 ) 286 - 294 .

Norn C, Wicky BIM, Juergens D, Liu S, Kim D, Tischer D, Koepnick B, Anishchenko I et al. ( 2021 ) . Protein sequence design by conformational landscape optimization . Proceedings of the National Academy of Sciences of the United States of America vol. 118 , ( 11 )

Smets I, Reyes S, Baker D ( 2021 ) . Blunted vaccines responses after ocrelizumab highlight need for immunizations prior to treatment . Multiple Sclerosis and Related Disorders vol. 50 ,

Allen-Philbey K, De Trane S, Stennett A, Yildiz O, Adams A, Turner B, Marta M, Gnanapavan S et al. ( 2021 ) . Cladribine Personalised Dosing to Treat Active Multiple Sclerosis - Follow-up in 250 patients . MULTIPLE SCLEROSIS JOURNAL . vol. 27 , 90 - 91 .

Allen-Philbey K, De Trane S, Stennett A, Yildiz O, Adams A, Turner B, Marta M, Gnanapavan S et al. ( 2021 ) . Cladribine personalised dosing for active multiple sclerosis: BartsMS cohort follow-up . NEUROLOGY . vol. 96 ,

Smets I, Holden D, Bianchi L, Ammoscato F, Allen-Philbey K, Baker D, Turner B, Marta M et al. ( 2021 ) . Factors contributing to CSF NfL reduction over time in people with multiple sclerosis starting treatment: an observational study . MULTIPLE SCLEROSIS JOURNAL . vol. 27 , 514 - 515 .

Bqain M, Efimov A, Baker D, Kang AS ( 2021 ) . Immunogenicity of biologics used in the treatment of inflammatory bowel disease . Human Antibodies vol. 29 , ( 4 ) 225 - 235 .

Patel V, Efimov A, Baker D, Kang AS ( 2021 ) . Immunogenicity of biologics used in the treatment of moderate to severe psoriasis . Human Antibodies vol. 29 , ( 3 ) 171 - 178 .

Vickaryous N, Asardag AN, Chance R, Jones M, Bestwick J, Shah SN, George K, Schmierer K et al. ( 2021 ) . Seroconversion following vaccination against SARS-CoV-2 in people with MS: impact of disease modifying therapy . MULTIPLE SCLEROSIS JOURNAL vol. 27 , ( 2_SUPPL ) 775 - 776 .

Allen-Philbey K, De Trane S, Stennett A, Yildiz O, Adams A, Turner B, Marta M, Gnanapavan S et al. ( 2021 ) . Up to 6 years follow-up of people with MS (n=250) receiving cladribine . MULTIPLE SCLEROSIS JOURNAL . vol. 27 , 546 - 547 .

Guo L, Gregson A, Baker D, Selwood D, Cordeiro MF ( 2021 ) . VSN16S, an agonist of the cannabinoid receptor, reduces IOP profiles and exhibits neuroprotective properties in a rat model of glaucoma . INVESTIGATIVE OPHTHALMOLOGY & VISUAL SCIENCE . vol. 62 ,

Thomson A, Dobson R, Baker D, Giovannoni G ( 2020 ) . Digesting science: Developing educational activities about multiple sclerosis, prevention and treatment to increase the confidence of affected families . Multiple Sclerosis and Related Disorders vol. 47 ,

Cunniffe N, Vuong KA, Ainslie D, Baker D, Beveridge J, Bickley S, Camilleri P, Craner M et al. ( 2020 ) . Systematic approach to selecting licensed drugs for repurposing in the treatment of progressive multiple sclerosis . Journal of Neurology Neurosurgery & Psychiatry vol. 92 , ( 3 ) 295 - 302 .

Amor S, Blanco LF ( 2020 ) . Innate immunity during SARS-CoV-2: evasion strategies and activation trigger hypoxia and vascular damage . Clinical & Experimental Immunology vol. 202 , ( 2 ) 193 - 209 .

Mateo-Casas M, Reyes S, De Trane S, Anjorin G, Baker D, Giovannoni G ( 2020 ) . Severe lymphopenia after subcutaneous cladribine in a patient with multiple sclerosis: To vaccinate or not? . eNeurologicalSci vol. 21 ,

Jacobs BM, Taylor T, Awad A, Baker D, Giovanonni G, Noyce AJ, Dobson R ( 2020 ) . Summary-data-based Mendelian randomization prioritizes potential druggable targets for multiple sclerosis . Brain Communications vol. 2 , ( 2 )

Baker D, Roberts CAK, Pryce G, Kang AS, Marta M, Reyes S, Schmierer K, Giovannoni G et al. ( 2020 ) . COVID-19 vaccine-readiness for anti-CD20-depleting therapy in autoimmune diseases . Clinical & Experimental Immunology vol. 202 , ( 2 ) 149 - 161 .

Petrova N, Nutma E, Carassiti D, Newman JR, Amor S, Baker D ( 2020 ) . Synaptic Loss in Multiple Sclerosis Spinal Cord . Annals of Neurology vol. 88 , ( 3 ) 619 - 625 .

Licht-Mayer S, Campbell GR, Canizares M, Mehta AR, Gane AB, McGill K, Ghosh A, Fullerton A et al. ( 2020 ) . Enhanced axonal response of mitochondria to demyelination offers neuroprotection: implications for multiple sclerosis . Acta Neuropathologica vol. 140 , ( 2 ) 143 - 167 .

Baker D, Pryce G, James LK, Marta M, Schmierer K ( 2020 ) . The ocrelizumab phase II extension trial suggests the potential to improve the risk: Benefit balance in multiple sclerosis . Multiple Sclerosis and Related Disorders vol. 44 ,

Saxena G, Moore JM, Jones M, Pryce G, Ali L, Leisegang GR, Vijay V, Loveless S et al. ( 2020 ) . Detecting and predicting neutralization of alemtuzumab responses in MS . Neurology Neuroimmunology & Neuroinflammation vol. 7 , ( 4 )

Amor S, Baker D, Khoury SJ ( 2020 ) . SARS‐CoV‐2 and Multiple Sclerosis: Not All Immune Depleting DMTs are Equal or Bad . Annals of Neurology vol. 87 , ( 6 ) 794 - 797 .

Baker D, Amor S, Kang AS, Schmierer K, Giovannoni G ( 2020 ) . The underpinning biology relating to multiple sclerosis disease modifying treatments during the COVID-19 pandemic . Multiple Sclerosis and Related Disorders vol. 43 ,

Mateo-Casas M, Reyes S, O'Toole EA, De Trane S, Yildiz O, Allen-Philbey K, Mathews J ( 2020 ) . Severe skin reactions associated with cladribine in people with multiple sclerosis . Multiple Sclerosis and Related Disorders . vol. 43 ,

Munger K, Kang A, Baker D, Goodman A, Samkoff L ( 2020 ) . Alemtuzumab Depletion Failure and Neutralizing Anti-Drug Antibodies: a Case Report and Call for Monitoring (1347) . Neurology vol. 94 , ( 15_supplement )

Schmierer K, Baker D ( 2020 ) . B cells and multiple sclerosis spinal cord pathology . Brain Pathology vol. 30 , ( 4 ) 730 - 731 .

Bertrand JA, Schicht M, Stamer WD, Baker D, Sherwood JM ( 2020 ) . The β4-Subunit of the Large-Conductance Potassium Ion Channel KCa1.1 Regulates Outflow Facility in Mice . Investigative Ophthalmology & Visual Science vol. 61 , ( 3 ) 41 - 41 .

Ali L, Saxena G, Jones M, Leisegang GR, Gammon L, Gnanapavan S, Giovannoni G, Schmierer K et al. ( 2020 ) . A cell-based assay for the detection of neutralizing antibodies against alemtuzumab . BioTechniques vol. 68 , ( 4 ) 185 - 190 .

Baker D, Ali L, Saxena G, Pryce G, Jones M, Schmierer K, Giovannoni G, Gnanapavan S et al. ( 2020 ) . The Irony of Humanization: Alemtuzumab, the First, But One of the Most Immunogenic, Humanized Monoclonal Antibodies . Frontiers in Immunology vol. 11 ,

Saxena GK, Theocharopoulos I, Aziz NT, Jones M, Gnanapavan S, Giovannoni G, Schmierer K, Garnett JA et al. ( 2020 ) . GloBody Technology: Detecting Anti-Drug Antibody against VH/VL domains . Scientific Reports vol. 10 , ( 1 ) Article 1860 ,

Baker D, Pryce G, James LK, Marta M, Schmierer K ( 2020 ) . The ocrelizumab phase II extension trial suggests the potential to improve the risk:benefit balance in multiple sclerosis .

Baker D ( 2020 ) . Complexity in the Future: Far-from-Equilibrium Systems and Strategic Foresight . The 21st Century Singularity and Global Futures , Springer Nature

Ghobril AN, Baker D, Rokop N, Carlson CR ( 2020 ) . Para Além dos Cursos de Empreendedorismo: estratégia, estrutura e processos na Illinois tech para se tornar uma universidade empreendedora . REGEPE Entrepreneurship and Small Business Journal vol. 9 , ( 1 ) 42 - 76 .

Munger K, Kang A, Baker D, Goodman A, Samkoff L ( 2020 ) . Alemtuzumab depletion failure and neutralizing anti-drug antibodies: a case report and call for monitoring . MULTIPLE SCLEROSIS JOURNAL . vol. 26 , 258 - 258 .

Baker DJ ( 2020 ) . Artificial Ventilation, A Basic Clinical Guide . Springer Nature

Allen-Philbey K, De Trane S, Stennett A, Yildiz O, Adams A, Turner B, Marta M, Gnanapavan S et al. ( 2020 ) . Cladribine personalised dosing to treat multiple sclerosis: observations in 208 patients . MULTIPLE SCLEROSIS JOURNAL . vol. 26 , 522 - 523 .

Lieberman D, Mangat H, Allen-Philbey K, Baker D, Barkhof F, Chandran S, Chapman C, Chataway J et al. ( 2020 ) . Cladribine to halt deterioration in people with advanced multiple sclerosis (CHARIOTMS) . MULTIPLE SCLEROSIS JOURNAL . vol. 26 , 212 - 213 .

Yager P, Abe K, Anderson CE, Baker D, Belousov Y, Bishop J, Buser JR, Byrnes SA et al. ( 2020 ) . Low-cost disposable point-of-care devices based on porous materials for rapid detection of pathogens . 21st International Conference on Miniaturized Systems for Chemistry and Life Sciences Microtas 2017 . 97 - 100 .

Baker D, Pryce G, James LK, Schmierer K, Giovannoni G ( 2019 ) . Failed B cell survival factor trials support the importance of memory B cells in multiple sclerosis . European Journal of Neurology vol. 27 , ( 2 ) 221 - 228 .

Farrell R, Baker D ( 2019 ) . An expert opinion: Optimisation of pharmacological management of multiple sclerosis related spasticity . Advances in Clinical Neuroscience and Rehabilitation vol. 18 , ( 5 ) 17 - 19 .

Baker D, Nutma E, O'Shea H, Cooke A ( 2019 ) . Autoimmune encephalomyelitis in NOD mice is not initially a progressive multiple sclerosis model . Annals of Clinical and Translational Neurology vol. 6 , ( 8 ) 1362 - 1372 .

Batcheller L ( 2019 ) . Cost of disease modifying therapies for multiple sclerosis: Is front-loading the answer? . Journal of the Neurological Sciences vol. 404 , 19 - 28 .

Tabatabaee S, Baker D, Selwood DL, Whalley BJ ( 2019 ) . The Cannabinoid-Like Compound, VSN16R, Acts on Large Conductance, Ca2+-Activated K+ Channels to Modulate Hippocampal CA1 Pyramidal Neuron Firing . Pharmaceuticals vol. 12 , ( 3 )

Baker D, Jacobs BM, Gnanapavan S, Schmierer K, Giovannoni G ( 2019 ) . Plasma cell and B cell-targeted treatments for use in advanced multiple sclerosis . Multiple Sclerosis and Related Disorders vol. 35 , 19 - 25 .

Pryce G, Baker D ( 2019 ) . CHAPTER 11 Cannabinoids as a Therapeutic Approach in Multiple Sclerosis . Emerging Drugs and Targets for Multiple Sclerosis , Royal Society of Chemistry (RSC)

De Trane S, Mao Z, Alvarez-Gonzalez C, Allen-Philbey K, Yildiz O, Campion T, Adams A, Turner B et al. ( 2019 ) . Cladribine to treat Relapsing and Progressive Multiple Sclerosis - experience in >200 patients (S26.008) . Neurology vol. 92 , ( 15_supplement )

Baker D ( 2019 ) . What has de novo protein design taught us about protein folding and biophysics? . Protein Science vol. 28 , ( 4 ) 678 - 683 .

Basak S, Nobrega RP, Tavella D, Deveau LM, Koga N, Tatsumi-Koga R, Baker D, Massi F et al. ( 2019 ) . Networks of electrostatic and hydrophobic interactions modulate the complex folding free energy surface of a designed βα protein . Proceedings of the National Academy of Sciences of the United States of America vol. 116 , ( 14 ) 6806 - 6811 .

Marcandalli J, Fiala B, Ols S, Perotti M, de van der Schueren W, Snijder J, Hodge E, Benhaim M et al. ( 2019 ) . Induction of Potent Neutralizing Antibody Responses by a Designed Protein Nanoparticle Vaccine for Respiratory Syncytial Virus . Cell vol. 176 , ( 6 ) 1420 - 1431.e17 .

Baker D, Pryce G, Herrod SS ( 2019 ) . Potential mechanisms of action related to the efficacy and safety of cladribine . Multiple Sclerosis and Related Disorders vol. 30 , 176 - 186 .

Valliere MA, Korman TP, Woodall NB, Khitrov GA, Taylor RE, Baker D, Bowie JU ( 2019 ) . A cell-free platform for the prenylation of natural products and application to cannabinoid production . Nature Communications vol. 10 , ( 1 )

Silva D-A, Yu S, Ulge UY, Spangler JB, Jude KM, Labão-Almeida C, Ali LR, Quijano-Rubio A et al. ( 2019 ) . De novo design of potent and selective mimics of IL-2 and IL-15 . Nature vol. 565 , ( 7738 ) 186 - 191 .

Anderson CE, Buser JR, Fleming AM, Strauch E-M, Ladd PD, Englund J, Baker D, Yager P ( 2019 ) . An integrated device for the rapid and sensitive detection of the influenza hemagglutinin . Lab on a Chip vol. 19 , ( 5 ) 885 - 896 .

Pryce G ( 2019 ) . CHAPTER 11: Cannabinoids as a Therapeutic Approach in Multiple Sclerosis . Rsc Drug Discovery Series , vol. 2019-January ,

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Dubuisson N, Marta M, Gnanapavan S, Turner B, Baker D, Thomson A, Schmierer K, Giovannoni G ( 2018 ) . Inclusion criteria used in trials of people with progressive multiple sclerosis . Multiple Sclerosis Journal vol. 26 , ( 3 ) 279 - 283 .

Maguire JB, Boyken SE, Baker D ( 2018 ) . Correction to Rapid Sampling of Hydrogen Bond Networks for Computational Protein Design . Journal of Chemical Theory and Computation vol. 14 , ( 10 ) 5434 - 5434 .

Dou J, Vorobieva AA, Sheffler W, Doyle LA, Park H, Bick MJ, Mao B, Foight GW et al. ( 2018 ) . De novo design of a fluorescence-activating β-barrel . Nature vol. 561 , ( 7724 ) 485 - 491 .

Baker D, Pryce G, Amor S, Giovannoni G ( 2018 ) . Learning from other autoimmunities to understand targeting of B cells to control multiple sclerosis . Brain vol. 141 , ( 10 ) 2834 - 2847 .

Jester BW, Tinberg CE, Rich MS, Baker D, Fields S ( 2018 ) . Engineered Biosensors from Dimeric Ligand-Binding Domains . ACS Synthetic Biology vol. 7 , ( 10 ) 2457 - 2467 .

Gushchina S, Pryce G, Yip PK, Giovannoni G, Bo X ( 2018 ) . Increased expression of colony‐stimulating factor‐1 in mouse spinal cord with experimental autoimmune encephalomyelitis correlates with microglial activation and neuronal loss . Glia vol. 66 , ( 10 ) 2108 - 2125 .

Pryce G, Baker D ( 2018 ) . Oligoclonal bands in multiple sclerosis; Functional significance and therapeutic implications. Does the specificity matter? . Multiple Sclerosis and Related Disorders vol. 25 , 131 - 137 .

Bavinton BR, Pinto AN, Phanuphak N, Grinsztejn B, Prestage GP, Zablotska-Manos IB, Jin F, Fairley CK et al. ( 2018 ) . Viral suppression and HIV transmission in serodiscordant male couples: an international, prospective, observational, cohort study . The Lancet HIV vol. 5 , ( 8 ) e438 - e447 .

Jacobs BM, Ammoscato F, Giovannoni G, Baker D, Schmierer K ( 2018 ) . Cladribine: mechanisms and mysteries in multiple sclerosis . Journal of Neurology Neurosurgery & Psychiatry vol. 89 , ( 12 )

Lau Y-TK, Baytshtok V, Howard TA, Fiala BM, Johnson JM, Carter LP, Baker D, Lima CD et al. ( 2018 ) . Discovery and engineering of enhanced SUMO protease enzymes . Journal of Biological Chemistry vol. 293 , ( 34 ) 13224 - 13233 .

Keasar C, McGuffin LJ, Wallner B, Chopra G, Adhikari B, Bhattacharya D, Blake L, Bortot LO et al. ( 2018 ) . An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12 . Scientific Reports vol. 8 , ( 1 )

Geiger-Schuller K, Sforza K, Yuhas M, Parmeggiani F, Baker D, Barrick D ( 2018 ) . Extreme stability in de novo-designed repeat arrays is determined by unusually stable short-range interactions . Proceedings of the National Academy of Sciences of the United States of America vol. 115 , ( 29 ) 7539 - 7544 .

Mao Z, Álvarez-Gonzalez C, De Trane S, Yildiz O, Albor C, Doctor G, Soon D, Pepper G et al. ( 2018 ) . Cladribine: Off-label disease modification for people with multiple sclerosis in resource-poor settings? . Multiple Sclerosis Journal - Experimental Translational and Clinical vol. 4 , ( 2 )

Yildiz O, Mao Z, Adams A, Dubuisson N, Giovannoni G, Malaspina A, Baker D ( 2018 ) . Disease activity in progressive multiple sclerosis can be effectively reduced by cladribine . Multiple Sclerosis and Related Disorders vol. 24 , 20 - 27 .

Nicholson T, Church C, Baker DJ ( 2018 ) . The role of adipokines in skeletal muscle inflammation and insulin sensitivity . Journal of Inflammation vol. 15 , ( 1 )

Maguire JB, Boyken SE, Baker D, Kuhlman B ( 2018 ) . Rapid Sampling of Hydrogen Bond Networks for Computational Protein Design . Journal of Chemical Theory and Computation vol. 14 , ( 5 ) 2751 - 2760 .

Ceronie B, Dubuisson N, Ammoscato F, Baker D ( 2018 ) . Memory B Cells: Toward a Unified Therapeutic Target for Effective Immunotherapy in Multiple Sclerosis (P5.365) . Neurology . vol. 90 ,

Ceronie B, Jacobs BM, Baker D, Dubuisson N, Mao Z, Ammoscato F, Lock H, Longhurst HJ et al. ( 2018 ) . Cladribine treatment of multiple sclerosis is associated with depletion of memory B cells . Journal of Neurology vol. 265 , ( 5 ) 1199 - 1209 .

Ruz‐Maldonado I, Pingitore A, Liu B, Atanes P, Huang GC, Baker D, Alonso FJ ( 2018 ) . Cover Image, Volume 20, Issue 4 . Diabetes Obesity and Metabolism vol. 20 , ( 4 ) i - i .

Crook ZR, Sevilla GP, Friend D, Brusniak M-Y, Bandaranayake AD, Clarke M, Gewe M, Mhyre AJ et al. ( 2018 ) . Publisher Correction: Mammalian display screening of diverse cystine-dense peptides for difficult to drug targets . Nature Communications vol. 9 , ( 1 )

Silva D, Stewart L, Lam K, Jin R, Baker D ( 2018 ) . Structures and disulfide cross‐linking of de novo designed therapeutic mini‐proteins . The FEBS Journal vol. 285 , ( 10 ) 1783 - 1785 .

Park H, Ovchinnikov S, Kim DE, DiMaio F, Baker D ( 2018 ) . Protein homology model refinement by large-scale energy optimization . Proceedings of the National Academy of Sciences of the United States of America vol. 115 , ( 12 ) 3054 - 3059 .

Sutherland MC, Jarodsky JM, Ovchinnikov S, Baker D, Kranz RG ( 2018 ) . Structurally Mapping Endogenous Heme in the CcmCDE Membrane Complex for Cytochrome c Biogenesis . Journal of Molecular Biology vol. 430 , ( 8 ) 1065 - 1080 .

Lu P, Min D, DiMaio F, Wei KY, Vahey MD, Boyken SE, Chen Z, Fallas JA et al. ( 2018 ) . Accurate computational design of multipass transmembrane proteins . Science vol. 359 , ( 6379 ) 1042 - 1046 .

Sockolosky JT, Trotta E, Parisi G, Picton L, Su LL, Le AC, Chhabra A, Silveria SL et al. ( 2018 ) . Selective targeting of engineered T cells using orthogonal IL-2 cytokine-receptor complexes . Science vol. 359 , ( 6379 ) 1037 - 1042 .

Sahasrabuddhe A, Hsia Y, Busch F, Sheffler W, King NP, Baker D, Wysocki VH ( 2018 ) . Confirmation of intersubunit connectivity and topology of designed protein complexes by native MS . Proceedings of the National Academy of Sciences of the United States of America vol. 115 , ( 6 ) 1268 - 1273 .

Ruz‐Maldonado I, Pingitore A, Atanes P, Huang GC, Baker D, Persaud SJ ( 2018 ) . LH‐21 and abnormal cannabidiol improve β‐cell function in isolated human and mouse islets through GPR55‐dependent and ‐independent signalling . Diabetes Obesity and Metabolism vol. 20 , ( 4 ) 930 - 942 .

Dubuisson N, Baker D, Kang AS, Pryce G, Marta M, Visser LH, Hofmann WE, Gnanapavan S et al. ( 2018 ) . Alemtuzumab depletion failure can occur in multiple sclerosis . Immunology vol. 154 , ( 2 ) 253 - 260 .

Ruz-Maldonado I, Liu B, Atanes P, Pingitore A, Huang GC ( 2018 ) . CB1 antagonists SR141617A and AM251 stimulate insulin secretion from mouse and human islets . DIABETIC MEDICINE . vol. 35 , 47 - 47 .

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Yildiz O, Mao Z, Adams A, Dubuisson N, Allen-Philbey K, Giovannoni G, Baker D, Gnanapavan S ( 2018 ) . Elevated neurofilament light chain levels in progressive multiple sclerosis effectively reduced by cladribine treatment . MULTIPLE SCLEROSIS JOURNAL . vol. 24 , 949 - 949 .

Van Patten WJ, Walder R, Adhikari A, Okoniewski SR, Ravichandran R, Tinberg CE, Baker D, Perkins TT ( 2017 ) . Improved Free‐Energy Landscape Quantification Illustrated with a Computationally Designed Protein–Ligand Interaction . ChemPhysChem vol. 19 , ( 1 ) 5 - 5 .

Crook ZR, Sevilla GP, Friend D, Brusniak M-Y, Bandaranayake AD, Clarke M, Gewe M, Mhyre AJ et al. ( 2017 ) . Mammalian display screening of diverse cystine-dense peptides for difficult to drug targets . Nature Communications vol. 8 , ( 1 )

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Nordenfelt P, Moore TI, Mehta SB, Kalappurakkal JM, Swaminathan V, Koga N, Lambert TJ, Baker D et al. ( 2017 ) . Direction of actin flow dictates integrin LFA-1 orientation during leukocyte migration . Nature Communications vol. 8 , ( 1 )

Van Patten WJ, Walder R, Adhikari A, Okoniewski SR, Ravichandran R, Tinberg CE, Baker D, Perkins TT ( 2017 ) . Improved Free‐Energy Landscape Quantification Illustrated with a Computationally Designed Protein–Ligand Interaction . ChemPhysChem vol. 19 , ( 1 ) 19 - 23 .

Dubuisson N, Bauer A, Marta M, Gnanapavan S, Turner B, Baker D, Giovannoni G, Schmierer K et al. ( 2017 ) . PO124 Validation of an environmentally-friendly and affordable cardboard 9-hole peg test . Journal of Neurology Neurosurgery & Psychiatry . vol. 88 ,

Schmierer K, Marta M, Pryce G, Giovannoni G, Baker D ( 2017 ) . PO150 Memory b cells are key for immunotherapy in multiple sclerosis . Journal of Neurology Neurosurgery & Psychiatry . vol. 88 , a52 - a52 .

Younger D, Berger S, Baker D, Klavins E ( 2017 ) . High-throughput characterization of protein–protein interactions by reprogramming yeast mating . Proceedings of the National Academy of Sciences of the United States of America vol. 114 , ( 46 ) 12166 - 12171 .

Dou J, Doyle L, Greisen PJ, Schena A, Park H, Johnsson K, Stoddard BL, Baker D ( 2017 ) . Sampling and energy evaluation challenges in ligand binding protein design . Protein Science vol. 26 , ( 12 ) 2426 - 2437 .

Lin Y, Koga N, Vorobiev SM, Baker D ( 2017 ) . Cyclic oligomer design with de novo αβ‐proteins . Protein Science vol. 26 , ( 11 ) 2187 - 2194 .

Baker D, Giovannoni G ( 2017 ) . Marked neutropenia: significant but rare in people with multiple sclerosis after alemtuzumab treatment . Multiple Sclerosis and Related Disorders

Park H, Kim DE, Ovchinnikov S, Baker D, DiMaio F ( 2017 ) . Automatic structure prediction of oligomeric assemblies using Robetta in CASP12 . Proteins Structure Function and Bioinformatics vol. 86 , ( S1 ) 283 - 291 .

Ovchinnikov S, Park H, Kim DE, DiMaio F, Baker D ( 2017 ) . Protein structure prediction using Rosetta in CASP12 . Proteins Structure Function and Bioinformatics vol. 86 , ( Suppl 1 ) 113 - 121 .

Swaminathan V, Kalappurakkal JM, Mehta SB, Nordenfelt P, Moore TI, Koga N, Baker DA, Oldenbourg R et al. ( 2017 ) . Actin retrograde flow actively aligns and orients ligand-engaged integrins in focal adhesions . Proceedings of the National Academy of Sciences of the United States of America vol. 114 , ( 40 ) 10648 - 10653 .

Chevalier A, Silva D-A, Rocklin GJ, Hicks DR, Vergara R, Murapa P, Bernard SM, Zhang L et al. ( 2017 ) . Massively parallel de novo protein design for targeted therapeutics . Nature vol. 550 , ( 7674 ) 74 - 79 .

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Pryce G, Baker D ( 2017 ) . Antidote to cannabinoid intoxication: the CB1 receptor inverse agonist, AM251, reverses hypothermic effects of the CB1 receptor agonist, CB‐13, in mice . British Journal of Pharmacology vol. 174 , ( 21 ) 3790 - 3794 .

Bick MJ, Greisen PJ, Morey KJ, Antunes MS, La D, Sankaran B, Reymond L, Johnsson K et al. ( 2017 ) . Computational design of environmental sensors for the potent opioid fentanyl . eLife vol. 6 ,

Yeh C-T, Brunette T, Baker D, McIntosh-Smith S, Parmeggiani F ( 2017 ) . Elfin: An algorithm for the computational design of custom three-dimensional structures from modular repeat protein building blocks . Journal of Structural Biology vol. 201 , ( 2 ) 100 - 107 .

Baker D, Herrod SS, Alvarez-Gonzalez C, Zalewski L ( 2017 ) . Both cladribine and alemtuzumab may affect MS via B-cell depletion (vol 4, e360, 2017) . NEUROLOGY-NEUROIMMUNOLOGY & NEUROINFLAMMATION vol. 4 , ( 5 )

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Anishchenko I, Ovchinnikov S, Kamisetty H, Baker D ( 2017 ) . Origins of coevolution between residues distant in protein 3D structures . Proceedings of the National Academy of Sciences of the United States of America vol. 114 , ( 34 ) 9122 - 9127 .

Baker D, Herrod SS, Alvarez-Gonzalez C ( 2017 ) . Interpreting Lymphocyte Reconstitution Data From the Pivotal Phase 3 Trials of Alemtuzumab . JAMA Neurol vol. 74 , ( 8 ) 961 - 969 .

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Baker D, Pryce G, Visintin C, Sisay S, Bondarenko AI, Ho WSV, Jackson SJ, Williams TE et al. ( 2017 ) . Big conductance calcium‐activated potassium channel openers control spasticity without sedation . British Journal of Pharmacology vol. 174 , ( 16 ) 2662 - 2681 .

Schoebel S, Mi W, Stein A, Ovchinnikov S, Pavlovicz R, DiMaio F, Baker D, Chambers MG et al. ( 2017 ) . Cryo-EM structure of the protein-conducting ERAD channel Hrd1 in complex with Hrd3 . Nature vol. 548 , ( 7667 ) 352 - 355 .

Dubuisson N, Baker D, Thomson A, Marta M, Gnanapavan S, Turner B, Giovannoni G, Schmierer K ( 2017 ) . Disease modification in advanced MS: Focus on upper limb function . Multiple Sclerosis Journal vol. 23 , ( 14 ) 1956 - 1957 .

Pillon MC, Sobhany M, Borgnia MJ, Williams JG, Stanley RE ( 2017 ) . Grc3 programs the essential endoribonuclease Las1 for specific RNA cleavage . Proceedings of the National Academy of Sciences of the United States of America vol. 114 , ( 28 ) e5530 - e5538 .

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Baker D, Herrod SS, Alvarez-Gonzalez C, Albor C ( 2017 ) . Both cladribine and alemtuzumab may effect MS via B-cell depletion . Neurology Neuroimmunology & Neuroinflammation vol. 4 , ( 4 )

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Anderson CE, Holstein CA, Strauch E-M, Bennett S, Chevalier A, Nelson J, Fu E, Baker D et al. ( 2017 ) . Rapid Diagnostic Assay for Intact Influenza Virus Using a High Affinity Hemagglutinin Binding Protein . Analytical Chemistry vol. 89 , ( 12 ) 6608 - 6615 .

Alvarez‐Gonzalez C, Adams A, Mathews J, Turner BP, Giovannoni G ( 2017 ) . Cladribine to treat disease exacerbation after fingolimod discontinuation in progressive multiple sclerosis . Annals of Clinical and Translational Neurology vol. 4 , ( 7 ) 506 - 511 .

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Kleffner R, Flatten J, Leaver-Fay A, Baker D, Siegel JB, Khatib F, Cooper S ( 2017 ) . Foldit Standalone: a video game-derived protein structure manipulation interface using Rosetta . Bioinformatics vol. 33 , ( 17 ) 2765 - 2767 .

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Lecommandeur E, Baker D, Cox TM, Griffin JL ( 2017 ) . Alterations in endo-lysosomal function induce similar hepatic lipid profiles in rodent models of drug-induced phospholipidosis and Sandhoff disease . Journal of Lipid Research vol. 58 , ( 7 ) 1306 - 1314 .

Sefia E, Pryce G, Meier U-C, Giovannoni G ( 2017 ) . Depletion of CD20 B cells fails to inhibit relapsing mouse experimental autoimmune encephalomyelitis . Multiple Sclerosis and Related Disorders vol. 14 , 46 - 50 .

Goldsmith M, Aggarwal N, Ashani Y, Jubran H, Greisen PJ, Ovchinnikov S, Leader H, Baker D et al. ( 2017 ) . Overcoming an optimization plateau in the directed evolution of highly efficient nerve agent bioscavengers . Protein Engineering Design and Selection vol. 30 , ( 4 ) 333 - 345 .

Baker D, Marta M, Pryce G, Giovannoni G, Schmierer K ( 2017 ) . Memory B Cells are Major Targets for Effective Immunotherapy in Relapsing Multiple Sclerosis . EBioMedicine vol. 16 , 41 - 50 .

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Baker D, Kang AS, Gnanapavan S, Giovannoni G, Schmierer K ( 2017 ) . A central role of B cells in MS control and causing autoimmunity after alemtuzumab . MULTIPLE SCLEROSIS JOURNAL . vol. 23 , 336 - 336 .

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Phippen SW, Stevens CA, Vance TDR, King NP, Baker D, Davies PL ( 2016 ) . Multivalent Display of Antifreeze Proteins by Fusion to Self-Assembling Protein Cages Enhances Ice-Binding Activities . Biochemistry vol. 55 , ( 49 ) 6811 - 6820 .

Rose JC, Huang P-S, Camp ND, Ye J, Leidal AM, Goreshnik I, Trevillian BM, Dickinson MS et al. ( 2016 ) . A computationally engineered RAS rheostat reveals RAS–ERK signaling dynamics . Nature Chemical Biology vol. 13 , ( 1 ) 119 - 126 .

Alvarez-Gonzalez C, Allen-Philbey K, Mathews J, Turner, Baker D, Gnanapavan S, Marta M, Giovannoni G et al. ( 2016 ) . TREATING MULTIPLE SCLEROSIS WITH CLADRIBINE . Journal of Neurology Neurosurgery & Psychiatry . vol. 87 ,

Park H, Bradley P, Greisen P, Liu Y, Mulligan VK, Kim DE, Baker D, DiMaio F ( 2016 ) . Simultaneous Optimization of Biomolecular Energy Functions on Features from Small Molecules and Macromolecules . Journal of Chemical Theory and Computation vol. 12 , ( 12 ) 6201 - 6212 .

Berger S, Procko E, Margineantu D, Lee EF, Shen BW, Zelter A, Silva D-A, Chawla K et al. ( 2016 ) . Computationally designed high specificity inhibitors delineate the roles of BCL2 family proteins in cancer . eLife vol. 5 ,

Baker D, Anandhakrishnan A, Tuite-Dalton KA, Middleton RM, Giovannoni G ( 2016 ) . How to refer to people with disease in research outputs: The disconnection between academic practise and that preferred by people with multiple sclerosis . Multiple Sclerosis and Related Disorders vol. 10 , 127 - 133 .

Liu B, Song S, Ruz-Maldonado I, Pingitore A, Baker D, Jones PM ( 2016 ) . GPR55‐dependent stimulation of insulin secretion from isolated mouse and human islets of Langerhans . Diabetes Obesity and Metabolism vol. 18 , ( 12 ) 1263 - 1273 .

Chen J, Varga A, Selvarajah S, Jenes A, Dienes B, Veress G, Brain SD, Baker D et al. ( 2016 ) . Spatial Distribution of the Cannabinoid Type 1 and Capsaicin Receptors May Contribute to the Complexity of Their Crosstalk . Scientific Reports vol. 6 , ( 1 )

Reichen C, Hansen S, Forzani C, Honegger A, Fleishman SJ, Zhou T, Parmeggiani F, Ernst P et al. ( 2016 ) . Computationally Designed Armadillo Repeat Proteins for Modular Peptide Recognition . Journal of Molecular Biology vol. 428 , ( 22 ) 4467 - 4489 .

Garcia KE, Babanova S, Scheffler W, Hans M, Baker D, Atanassov P, Banta S ( 2016 ) . Designed protein aggregates entrapping carbon nanotubes for bioelectrochemical oxygen reduction . Biotechnology and Bioengineering vol. 113 , ( 11 ) 2321 - 2327 .

Horowitz S, Koepnick B, Martin R, Tymieniecki A, Cooper S, Flatten J, Rogawski DS, Koropatkin NM et al. ( 2016 ) . Determining crystal structures through crowdsourcing and coursework . Nature Communications vol. 7 , ( 1 )

Bhardwaj G, Mulligan VK, Bahl CD, Gilmore JM, Harvey PJ, Cheneval O, Buchko GW, Pulavarti SVSRK et al. ( 2016 ) . Accurate de novo design of hyperstable constrained peptides . Nature vol. 538 , ( 7625 ) 329 - 335 .

Huang P-S, Boyken SE, Baker D ( 2016 ) . The coming of age of de novo protein design . Nature vol. 537 , ( 7620 ) 320 - 327 .

Thomson A, Giovannoni G, Marta M, Gnanpavan S, Turner B, Baker D, Schmierer K ( 2016 ) . Importance of upper limb function in advanced multiple sclerosis . MULTIPLE SCLEROSIS JOURNAL . Conference: MSLondon (ACTRIMS/ECTRIMS) 2016 vol. 22 , 676 - 676 .

Rejdak K, Mitosek-Szewczyk K, Prus K, Trzciniecka O, Schmierer K ( 2016 ) . Induction therapy of relapsing secondary multiple sclerosis using generic cladribine . MULTIPLE SCLEROSIS JOURNAL . Conference: MSLondon (ACTRIMS/ECTRIMS) 2016 vol. 22 , 593 - 594 .

Petrova N, Scaravilli F, Baker D ( 2016 ) . Synaptic loss in the MS spinal cord: a key driver of disease progression? . MULTIPLE SCLEROSIS JOURNAL . Conference: ECTRIMS 2016 Committees ( UCL Institute of Neurology, London, UK ) from: 14/09/2016 to: 17/09/2016 , vol. 22 , 80 - 80 .

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Obexer R, Godina A, Garrabou X, Mittl PRE, Baker D, Griffiths AD, Hilvert D ( 2016 ) . Emergence of a catalytic tetrad during evolution of a highly active artificial aldolase . Nature Chemistry vol. 9 , ( 1 ) 50 - 56 .

Burnham SC, Rowe CC, Baker D, Bush AI, Doecke JD, Martins RN, Maruff P, Rainey-Smith S et al. ( 2016 ) . Predicting Alzheimer disease from a blood-based biomarker profile . Neurology vol. 87 , ( 11 ) 1093 - 1101 .

Peferoen LAN, Breur M, Peferoen-Baert R, Boddeke EHWGM, van der Valk P, Baker D, Amor S ( 2016 ) . Ageing and recurrent episodes of neuroinflammation promote progressive experimental autoimmune encephalomyelitis in Biozzi ABH mice . Immunology vol. 149 , ( 2 ) 146 - 156 .

Kaplan G, Lee F, Onda M, Kolyvas E, Bhardwaj G, Baker D, Pastan I ( 2016 ) . Protection of the Furin Cleavage Site in Low-Toxicity Immunotoxins Based on Pseudomonas Exotoxin A . Toxins vol. 8 , ( 8 )

Bale JB, Gonen S, Liu Y, Sheffler W, Ellis D, Thomas C, Cascio D, Yeates TO et al. ( 2016 ) . Accurate design of megadalton-scale two-component icosahedral protein complexes . Science vol. 353 , ( 6297 ) 389 - 394 .

Agahozo MC, Peferoen L, Baker D ( 2016 ) . CD20 therapies in multiple sclerosis and experimental autoimmune encephalomyelitis – Targeting T or B cells? . Multiple Sclerosis and Related Disorders vol. 9 , 110 - 117 .

Baird AL, Hye A, Westwood S, Ashton NJ, Bazenet C, Kiddle SJ, Ward M, Thambisetty M et al. ( 2016 ) . S4‐01‐01: Cross‐Sectional Studies of Plasma Proteomic Biomarkers Relating to Pet Amyloid and CSF Amyloid and Tau . Alzheimer's & Dementia vol. 12 , ( 7S_Part_6 ) p321 - p321 .

Sevastou I, Pryce G, Baker D, Selwood DL ( 2016 ) . Characterisation of Transcriptional Changes in the Spinal Cord of the Progressive Experimental Autoimmune Encephalomyelitis Biozzi ABH Mouse Model by RNA Sequencing . PLOS ONE vol. 11 , ( 6 )

Bolon DNA, Baker D, Tawfik DS ( 2016 ) . Editorial . Protein Science vol. 25 , ( 7 ) 1164 - 1167 .

Hsia Y, Bale JB, Gonen S, Shi D, Sheffler W, Fong KK, Nattermann U, Xu C et al. ( 2016 ) . Design of a hyperstable 60-subunit protein icosahedron . Nature vol. 535 , ( 7610 ) 136 - 139 .

Mak WS, Tran S, Marcheschi R, Bertolani S, Thompson J, Baker D, Liao JC, Siegel JB ( 2016 ) . Correction: Corrigendum: Integrative genomic mining for enzyme function to enable engineering of a non-natural biosynthetic pathway . Nature Communications vol. 7 , ( 1 )

( 2016 ) . Erratum for the Research Article “De novo design of protein homo-oligomers with modular hydrogen-bond network–mediated specificity” by S. E. Boyken, Z. Chen, B. Groves, R. A. Langan, G. Oberdorfer, A. Ford, J. M. Gilmore, C. Xu, F. DiMaio, J. Henrique Pereira, B. Sankaran, G. Seelig, P. H. Zwart, D. Baker . Science vol. 352 , ( 6288 ) aag1318 - aag1318 .

Heinze K, Sasaki E, King NP, Baker D, Hilvert D, Wuite GJL, Roos WH ( 2016 ) . Protein Nanocontainers from Nonviral Origin: Testing the Mechanics of Artificial and Natural Protein Cages by AFM . The Journal of Physical Chemistry B vol. 120 , ( 26 ) 5945 - 5952 .

Rödström KEJ, Regenthal P, Bahl C, Ford A, Baker D, Lindkvist-Petersson K ( 2016 ) . Two common structural motifs for TCR recognition by staphylococcal enterotoxins . Scientific Reports vol. 6 , ( 1 )

Boyken SE, Chen Z, Groves B, Langan RA, Oberdorfer G, Ford A, Gilmore JM, Xu C et al. ( 2016 ) . De novo design of protein homo-oligomers with modular hydrogen-bond network–mediated specificity . Science vol. 352 , ( 6286 ) 680 - 687 .

Basanta B, Chan KK, Barth P, King T, Sosnick TR, Hinshaw JR, Liu G, Everett JK et al. ( 2016 ) . Introduction of a polar core into the de novo designed protein Top7 . Protein Science vol. 25 , ( 7 ) 1299 - 1307 .

Ovchinnikov S, Park H, Kim DE, Liu Y, Wang RY, Baker D ( 2016 ) . Structure prediction using sparse simulated NOE restraints with Rosetta in CASP11 . Proteins Structure Function and Bioinformatics vol. 84 , ( Suppl 1 ) 181 - 188 .

Ovchinnikov S, Kim DE, Wang RY, Liu Y, DiMaio F, Baker D ( 2016 ) . Improved de novo structure prediction in CASP11 by incorporating coevolution information into Rosetta . Proteins Structure Function and Bioinformatics vol. 84 , ( Suppl 1 ) 67 - 75 .

Koday MT, Nelson J, Chevalier A, Koday M, Kalinoski H, Stewart L, Carter L, Nieusma T et al. ( 2016 ) . A Computationally Designed Hemagglutinin Stem-Binding Protein Provides In Vivo Protection from Influenza Independent of a Host Immune Response . PLOS Pathogens vol. 12 , ( 2 )

Aydin Z, Baker D, Noble WS ( 2015 ) . Template Scoring Methods for Protein Torsion Angle Prediction . Communications in Computer and Information Science . vol. 574 , 206 - 223 .

Anderson CE, Buser JR, Strauch EM, Marzan R, Baker D, Yager P ( 2016 ) . A two dimensional paper network for automated detection of the influenza virus employing computationally-designed affinity proteins . 20th International Conference on Miniaturized Systems for Chemistry and Life Sciences Microtas 2016 . 968 - 969 .

Baker DJ, Bradley N, Dobney A, Murray V, Meara JR, Cox CL ( 2016 ) . Human physiology, hazards and health risks . Clays Handbook of Environmental Health 21st Edition ,

Feng J, Jester BW, Tinberg CE, Mandell DJ, Antunes MS, Chari R, Morey KJ, Rios X et al. ( 2015 ) . A general strategy to construct small molecule biosensors in eukaryotes . eLife vol. 4 ,

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Warne J, Pryce G, Hill JM, Shi X, Lennerås F, Puentes F, Kip M, Hilditch L et al. ( 2015 ) . Selective Inhibition of the Mitochondrial Permeability Transition Pore Protects against Neurodegeneration in Experimental Multiple Sclerosis* . Journal of Biological Chemistry vol. 291 , ( 9 ) 4356 - 4373 .

Brunette T, Parmeggiani F, Huang P-S, Bhabha G, Ekiert DC, Tsutakawa SE, Hura GL, Tainer JA et al. ( 2015 ) . Exploring the repeat protein universe through computational protein design . Nature vol. 528 , ( 7583 ) 580 - 584 .

Doyle L, Hallinan J, Bolduc J, Parmeggiani F, Baker D, Stoddard BL, Bradley P ( 2015 ) . Rational design of α-helical tandem repeat proteins with closed architectures . Nature vol. 528 , ( 7583 ) 585 - 588 .

Ummenthum K, Peferoen LAN, Finardi A, Baker D, Pryce G, Mantovani A, Bsibsi M, Bottazzi B et al. ( 2015 ) . Pentraxin‐3 is upregulated in the central nervous system during MS and EAE, but does not modulate experimental neurological disease . European Journal of Immunology vol. 46 , ( 3 ) 701 - 711 .

King IC, Gleixner J, Doyle L, Kuzin A, Hunt JF, Xiao R, Montelione GT, Stoddard BL et al. ( 2015 ) . Precise assembly of complex beta sheet topologies from de novo designed building blocks . eLife vol. 4 ,

Goldsmith M, Eckstein S, Ashani Y, Greisen P, Leader H, Sussman JL, Aggarwal N, Ovchinnikov S et al. ( 2015 ) . Catalytic efficiencies of directly evolved phosphotriesterase variants with structurally different organophosphorus compounds in vitro . Archives of Toxicology vol. 90 , ( 11 ) 2711 - 2724 .

Mak WS, Tran S, Marcheschi R, Bertolani S, Thompson J, Baker D, Liao JC, Siegel JB ( 2015 ) . Integrative genomic mining for enzyme function to enable engineering of a non-natural biosynthetic pathway . Nature Communications vol. 6 , ( 1 )

Huang P-S, Feldmeier K, Parmeggiani F, Fernandez Velasco DA, Höcker B, Baker D ( 2015 ) . De novo design of a four-fold symmetric TIM-barrel protein with atomic-level accuracy . Nature Chemical Biology vol. 12 , ( 1 ) 29 - 34 .

Klein JC, Lajoie MJ, Schwartz JJ, Strauch E-M, Nelson J, Baker D, Shendure J ( 2015 ) . Multiplex pairwise assembly of array-derived DNA oligonucleotides . Nucleic Acids Research vol. 44 , ( 5 ) e43 - e43 .

Bednar D, Beerens K, Sebestova E, Bendl J, Khare S, Chaloupkova R, Prokop Z, Brezovsky J et al. ( 2015 ) . FireProt: Energy- and Evolution-Based Computational Design of Thermostable Multiple-Point Mutants . PLOS Computational Biology vol. 11 , ( 11 )

Baker DJ ( 2015 ) . Chapter 16 Acute Lung Injury Following Inhalation of Irritant Products of Combustion . Toxicology, Survival and Health Hazards of Combustion Products , Royal Society of Chemistry (RSC)

Smith RD, Damm-Ganamet KL, Dunbar JB, Ahmed A, Chinnaswamy K, Delproposto JE, Kubish GM, Tinberg CE et al. ( 2015 ) . CSAR Benchmark Exercise 2013: Evaluation of Results from a Combined Computational Protein Design, Docking, and Scoring/Ranking Challenge . Journal of Chemical Information and Modeling vol. 56 , ( 6 ) 1022 - 1031 .

Holstein CA, Chevalier A, Bennett S, Anderson CE, Keniston K, Olsen C, Li B, Bales B et al. ( 2015 ) . Immobilizing affinity proteins to nitrocellulose: a toolbox for paper-based assay developers . Analytical and Bioanalytical Chemistry vol. 408 , ( 5 ) 1335 - 1346 .

Pakpoor J, Disanto G, Altmann DR, Pavitt S, Turner BP, Marta M, Juliusson G, Baker D et al. ( 2015 ) . No evidence for higher risk of cancer in patients with multiple sclerosis taking cladribine . Neurology Neuroimmunology & Neuroinflammation vol. 2 , ( 6 )

Wolf C, Siegel JB, Tinberg C, Camarca A, Gianfrani C, Paski S, Guan R, Montelione G et al. ( 2015 ) . Engineering of Kuma030: A Gliadin Peptidase That Rapidly Degrades Immunogenic Gliadin Peptides in Gastric Conditions . Journal of the American Chemical Society vol. 137 , ( 40 ) 13106 - 13113 .

Lin Y-R, Koga N, Tatsumi-Koga R, Liu G, Clouser AF, Montelione GT, Baker D ( 2015 ) . Control over overall shape and size in de novo designed proteins . Proceedings of the National Academy of Sciences of the United States of America vol. 112 , ( 40 ) e5478 - e5485 .

Ovchinnikov S, Kinch L, Park H, Liao Y, Pei J, Kim DE, Kamisetty H, Grishin NV et al. ( 2015 ) . Large-scale determination of previously unsolved protein structures using evolutionary information . eLife vol. 4 ,

Park H, DiMaio F ( 2015 ) . CASP11 refinement experiments with ROSETTA . Proteins Structure Function and Bioinformatics vol. 84 , ( Suppl 1 ) 314 - 322 .

Heinisch T, Pellizzoni M, Dürrenberger M, Tinberg CE, Köhler V, Klehr J, Häussinger D, Baker D et al. ( 2015 ) . Improving the Catalytic Performance of an Artificial Metalloenzyme by Computational Design . Journal of the American Chemical Society vol. 137 , ( 32 ) 10414 - 10419 .

Bale JB, Park RU, Liu Y, Gonen S, Gonen T, Cascio D, King NP, Yeates TO et al. ( 2015 ) . Structure of a designed tetrahedral protein assembly variant engineered to have improved soluble expression . Protein Science vol. 24 , ( 10 ) 1695 - 1701 .

Poust S, Piety J, Bar‐Even A, Louw C, Baker D, Keasling JD, Siegel JB ( 2015 ) . Mechanistic Analysis of an Engineered Enzyme that Catalyzes the Formose Reaction . ChemBioChem vol. 16 , ( 13 ) 1950 - 1954 .

Blok NB, Tan D, Wang RY-R, Penczek PA, Baker D, DiMaio F, Rapoport TA, Walz T ( 2015 ) . Unique double-ring structure of the peroxisomal Pex1/Pex6 ATPase complex revealed by cryo-electron microscopy . Proceedings of the National Academy of Sciences of the United States of America vol. 112 , ( 30 ) e4017 - e4025 .

Gonen S, DiMaio F, Gonen T, Baker D ( 2015 ) . Design of ordered two-dimensional arrays mediated by noncovalent protein-protein interfaces . Science vol. 348 , ( 6241 ) 1365 - 1368 .

Ramaglia V, Jackson SJ, Neal JW ( 2015 ) . Complement activation and expression during chronic relapsing experimental autoimmune encephalomyelitis in the Biozzi ABH mouse . Clinical and Experimental Immunology vol. 180 , ( 3 ) 432 - 441 .

Matthaei JF, DiMaio F, Richards JJ, Pozzo LD, Baker D, Baneyx F ( 2015 ) . Designing Two-Dimensional Protein Arrays through Fusion of Multimers and Interface Mutations . Nano Letters vol. 15 , ( 8 ) 5235 - 5239 .

Antala S, Ovchinnikov S, Kamisetty H, Baker D, Dempski RE ( 2015 ) . Computation and Functional Studies Provide a Model for the Structure of the Zinc Transporter hZIP4* . Journal of Biological Chemistry vol. 290 , ( 29 ) 17796 - 17805 .

Park H, DiMaio F, Baker D ( 2015 ) . The Origin of Consistent Protein Structure Refinement from Structural Averaging . Structure vol. 23 , ( 6 ) 1123 - 1128 .

Ramaglia V, Jackson SJ, Hughes TR, Neal JW ( 2015 ) . Complement activation and expression during chronic relapsing experimental autoimmune encephalomyelitis in the Biozzi ABH mouse . Clinical & Experimental Immunology vol. 180 , ( 3 ) 432 - 441 .

Pryce G ( 2015 ) . Cannabinoids fail to show evidence of slowing down the progression of multiple sclerosis . BMJ Evidence-Based Medicine vol. 20 , ( 4 )

Browne L, Lidster K, Al-Izki S, Clutterbuck L, Posada C, Chan AWE, Baker D, Selwood DL ( 2015 ) . Correction to Imidazol-1-ylethylindazole Voltage-Gated Sodium Channel Ligands Are Neuroprotective during Optic Neuritis in a Mouse Model of Multiple Sclerosis . Journal of Medicinal Chemistry vol. 58 , ( 8 ) 3637 - 3637 .

Pakpoor J, Disanto G, Altmann D, Pavitt S, Turner B, Marta M, Juliusson G, Baker D et al. ( 2015 ) . Cancer Risk is Not Increased in People with Relapsing Multiple Sclerosis Taking Cladribine (P7.011) . Neurology vol. 84 , ( 14_supplement )

Siegel JB, Smith AL, Poust S, Wargacki AJ, Bar-Even A, Louw C, Shen BW, Eiben CB et al. ( 2015 ) . Computational protein design enables a novel one-carbon assimilation pathway . Proceedings of the National Academy of Sciences of the United States of America vol. 112 , ( 12 ) 3704 - 3709 .

Ashton NJ, Kiddle SJ, Graf J, Ward M, Baird AL, Hye A, Wong KV, Dobson RJ et al. ( 2015 ) . Blood protein predictors of brain amyloid for enrichment in clinical trials? . Alzheimer's & Dementia Diagnosis Assessment & Disease Monitoring vol. 1 , ( 1 ) 48 - 60 .

Wu D, Cerutti C, Lopez-Ramirez MA, Pryce G, King-Robson J, Simpson JE, van der Pol SM, de Vries HE et al. ( 2015 ) . Brain Endothelial miR-146a Negatively Modulates T-Cell Adhesion through Repressing Multiple Targets to Inhibit NF-κB Activation . Journal of cerebral blood flow and metabolism : official journal of the International Society of Cerebral Blood Flow and Metabolism vol. 35 , ( 3 ) 412 - 423 .

DiMaio F, Song Y, Li X, Brunner MJ, Xu C, Conticello V, Egelman E, Marlovits TC et al. ( 2015 ) . Atomic-accuracy models from 4.5-Å cryo-electron microscopy data with density-guided iterative local refinement . Nature Methods vol. 12 , ( 4 ) 361 - 365 .

Wang RY-R, Kudryashev M, Li X, Egelman EH, Basler M, Cheng Y, Baker D, DiMaio F ( 2015 ) . De novo protein structure determination from near-atomic-resolution cryo-EM maps . Nature Methods vol. 12 , ( 4 ) 335 - 338 .

Pearson AD, Mills JH, Song Y, Nasertorabi F, Han GW, Baker D, Stevens RC, Schultz PG ( 2015 ) . Trapping a transition state in a computationally designed protein bottle . Science vol. 347 , ( 6224 ) 863 - 867 .

Berguig GY, Convertine AJ, Frayo S, Kern HB, Procko E, Roy D, Srinivasan S, Margineantu DH et al. ( 2015 ) . Intracellular Delivery System for Antibody–Peptide Drug Conjugates . Molecular Therapy vol. 23 , ( 5 ) 907 - 917 .

Wijma HJ, Floor RJ, Bjelic S, Marrink SJ, Baker D, Janssen DB ( 2015 ) . Enantioselective Enzymes by Computational Design and In Silico Screening . Angewandte Chemie International Edition vol. 54 , ( 12 ) 3726 - 3730 .

Kudryashev M, Wang RY-R, Brackmann M, Scherer S, Maier T, Baker D, DiMaio F, Stahlberg H et al. ( 2015 ) . Structure of the Type VI Secretion System Contractile Sheath . Cell vol. 160 , ( 5 ) 952 - 962 .

O’Meara MJ, Leaver-Fay A, Tyka MD, Stein A, Houlihan K, DiMaio F, Bradley P, Kortemme T et al. ( 2015 ) . Combined Covalent-Electrostatic Model of Hydrogen Bonding Improves Structure Prediction with Rosetta . Journal of Chemical Theory and Computation vol. 11 , ( 2 ) 609 - 622 .

Biela A, Watkinson M, Meier UC, Baker D, Giovannoni G, Becer CR, Krause S ( 2015 ) . Disposable MMP-9 sensor based on the degradation of peptide cross-linked hydrogel films using electrochemical impedance spectroscopy . Biosensors and Bioelectronics vol. 68 , 660 - 667 .

Egelman EH, Xu C, DiMaio F, Magnotti E, Modlin C, Yu X, Wright E, Baker D et al. ( 2015 ) . Structural Plasticity of Helical Nanotubes Based on Coiled-Coil Assemblies . Structure vol. 23 , ( 2 ) 280 - 289 .

Morag O, Sgourakis NG, Baker D, Goldbourt A ( 2015 ) . The NMR–Rosetta capsid model of M13 bacteriophage reveals a quadrupled hydrophobic packing epitope . Proceedings of the National Academy of Sciences of the United States of America vol. 112 , ( 4 ) 971 - 976 .

Park K, Shen BW, Parmeggiani F, Huang P-S, Stoddard BL, Baker D ( 2015 ) . Control of repeat-protein curvature by computational protein design . Nature Structural & Molecular Biology vol. 22 , ( 2 ) 167 - 174 .

Wu D, Cerutti C, Lopez-Ramirez MA, Pryce G, King-Robson J, Simpson JE, Van Der Pol SMA, Baker D et al. ( 2015 ) . Brain endothelial miR-146a negatively modulates T-cell adhesion through repressing multiple targets to inhibit NF-κB activation . Journal of Perinatology vol. 35 , ( 3 ) 412 - 423 .

Aydin Z, Baker D, Noble WS ( 2015 ) . Constructing Structural Profiles for Protein Torsion Angle Prediction . Conference: Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms26 - 35 .

Pryce G, Baker D ( 2015 ) . Endocannabinoids in Multiple Sclerosis and Amyotrophic Lateral Sclerosis . Handbook of Experimental Pharmacology vol. 231 , 213 - 231 .

Vainchtein I, Vinet J, Al-Izki S, Pryce G, Grit C, Brouwer N, Amor S ( 2015 ) . Microglia are involved in apoptotic clearance during chronic-relapsing EAE . GLIA . vol. 63 , E353 - E353 .

Baker D, Amor S ( 2015 ) . Mouse models of multiple sclerosis: lost in translation? . Current Pharmaceutical Design vol. 21 , ( 18 ) 2440 - 2452 .

Ruz Maldonado I, Pingitore A, Liu B, Huang GC, Baker D, Persaud SJ ( 2015 ) . Stimulation of insulin secretion by cannabinoid ligands LH-21 and Abn-CBD in mouse and human islets: evaluation of the role of GPR55 . DIABETOLOGIA . vol. 58 , S86 - S86 .

Giovannoni G, Baker D ( 2015 ) . The problem with repurposing: Is there really an alternative to Big Pharma for developing new drugs for multiple sclerosis? . Multiple Sclerosis and Related Disorders vol. 4 , ( 1 ) 3 - 5 .

Pryce G, Riddall DR, Baker D ( 2014 ) . Neuroprotection in Experimental Autoimmune Encephalomyelitis and Progressive Multiple Sclerosis by Cannabis-Based Cannabinoids . Journal of Neuroimmune Pharmacology vol. 10 , ( 2 ) 281 - 292 .

Rossi P, Shi L, Liu G, Barbieri CM, Lee H, Grant TD, Luft JR, Xiao R et al. ( 2014 ) . A hybrid NMR/SAXS‐based approach for discriminating oligomeric protein interfaces using Rosetta . Proteins Structure Function and Bioinformatics vol. 83 , ( 2 ) 309 - 317 .

Bergeron JRC, Worrall LJ, De S, Sgourakis NG, Cheung AH, Lameignere E, Okon M, Wasney GA et al. ( 2014 ) . The Modular Structure of the Inner-Membrane Ring Component PrgK Facilitates Assembly of the Type III Secretion System Basal Body . Structure vol. 23 , ( 1 ) 161 - 172 .

Vittal V, Shi L, Wenzel DM, Scaglione KM, Duncan ED, Basrur V, Elenitoba-Johnson KSJ, Baker D et al. ( 2014 ) . Intrinsic disorder drives N-terminal ubiquitination by Ube2w . Nature Chemical Biology vol. 11 , ( 1 ) 83 - 89 .

Giovannoni G, Baker D, Schmierer K ( 2014 ) . The problem with repurposing: Is there really an alternative to Big Pharma for developing new drugs for multiple sclerosis? . Multiple Sclerosis and Related Disorders vol. 4 , ( 1 ) 3 - 5 .

Parmeggiani F, Huang P-S, Vorobiev S, Xiao R, Park K, Caprari S, Su M, Seetharaman J et al. ( 2014 ) . A General Computational Approach for Repeat Protein Design . Journal of Molecular Biology vol. 427 , ( 2 ) 563 - 575 .

Thyme SB, Song Y, Brunette TJ, Szeto MD, Kusak L, Bradley P, Baker D ( 2014 ) . Massively parallel determination and modeling of endonuclease substrate specificity . Nucleic Acids Research vol. 42 , ( 22 ) 13839 - 13852 .

Leblanc P, Moise L, Luza C, Chantaralawan K, Lezeau L, Yuan J, Field M, Richer D et al. ( 2014 ) . VaxCelerate II: Rapid development of a self-assembling vaccine for Lassa fever . Human Vaccines & Immunotherapeutics vol. 10 , ( 10 ) 3022 - 3038 .

Huang P-S, Oberdorfer G, Xu C, Pei XY, Nannenga BL, Rogers JM, DiMaio F, Gonen T et al. ( 2014 ) . High thermodynamic stability of parametrically designed helical bundles . Science vol. 346 , ( 6208 ) 481 - 485 .

Liu DS, Nivón LG, Richter F, Goldman PJ, Deerinck TJ, Yao JZ, Richardson D, Phipps WS et al. ( 2014 ) . Computational design of a red fluorophore ligase for site-specific protein labeling in living cells . Proceedings of the National Academy of Sciences of the United States of America vol. 111 , ( 43 ) e4551 - e4559 .

Holstein CA, Bennett S, Strauch E-M, Chevalier A, Fu E, Baker D, Yager P ( 2014 ) . Development of a Paper-Based Diagnostic for Influenza Detection . Conference: 2014 IEEE Healthcare Innovation Conference (HIC)296 - 299 .

Von Kutzleben S, Pryce G, Chretien N, Siders W ( 2014 ) . Inhibition of relapsing experimental autoimmune encephalomyelitis in Biozzi ABH mice using a mouse CD52-specific monoclonal antibody . Journal of Neuroimmunology . vol. 275 ,

Demers J-P, Habenstein B, Loquet A, Kumar Vasa S, Giller K, Becker S, Baker D, Lange A et al. ( 2014 ) . High-resolution structure of the Shigella type-III secretion needle by solid-state NMR and cryo-electron microscopy . Nature Communications vol. 5 , ( 1 )

Rosen LE, Connell KB, Marqusee S ( 2014 ) . Evidence for close side-chain packing in an early protein folding intermediate previously assumed to be a molten globule . Proceedings of the National Academy of Sciences of the United States of America vol. 111 , ( 41 ) 14746 - 14751 .

Giovannoni G, Baker D, Schmierer K ( 2014 ) . Simvastatin in patients with progressive multiple sclerosis . Lancet vol. 384 , ( 9947 )

Pakpoor J, Disanto G, Altmann DR, Pavitt S, Turner B, Calado-Marta M, Chataway J ( 2014 ) . CANCER RISK IN MULTIPLE SCLEROSIS PATIENTS TAKING CLADRIBINE . Journal of Neurology Neurosurgery & Psychiatry . vol. 85 , e4 - e4 .

Amor S, van der Star BJ, Bosca I, Raffel J, Gnanapavan S, Watchorn J, Kuhle J, Giovannoni G et al. ( 2014 ) . Neurofilament light antibodies in serum reflect response to natalizumab treatment in multiple sclerosis . Mult Scler vol. 20 , ( 10 ) 1355 - 1362 .

Graham DP, Rezai A, Baker D ( 2014 ) . The development and scalability of a high strength, damage tolerant, hybrid joining scheme for composite–metal structures . Composites Part A Applied Science and Manufacturing vol. 64 , 11 - 24 .

Kufareva I, Katritch V, 2013 POGD, Stevens RC, Abagyan R ( 2014 ) . Advances in GPCR Modeling Evaluated by the GPCR Dock 2013 Assessment: Meeting New Challenges . Structure vol. 22 , ( 8 ) 1120 - 1139 .

Woodhead J, Yang K, Brouwer K, Stahl S, Ambroso J, Watkins P ( 2014 ) . Mechanistic Modeling Reveals the Critical Knowledge Gaps in Bile Acid–Mediated DILI . CPT Pharmacometrics & Systems Pharmacology vol. 3 , ( 7 ) 1 - 8 .

Khoury GA, Liwo A, Khatib F, Zhou H, Chopra G, Bacardit J, Bortot LO, Faccioli RA et al. ( 2014 ) . WeFold: A coopetition for protein structure prediction . Proteins Structure Function and Bioinformatics vol. 82 , ( 9 ) 1850 - 1868 .

Magadán JG, Altman MO, Ince WL, Hickman HD, Stevens J, Chevalier A, Baker D, Wilson PC et al. ( 2014 ) . Biogenesis of Influenza A Virus Hemagglutinin Cross-Protective Stem Epitopes . PLOS Pathogens vol. 10 , ( 6 )

Griss R, Schena A, Reymond L, Patiny L, Werner D, Tinberg CE, Baker D, Johnsson K ( 2014 ) . Bioluminescent sensor proteins for point-of-care therapeutic drug monitoring . Nature Chemical Biology vol. 10 , ( 7 ) 598 - 603 .

Procko E, Berguig GY, Shen BW, Song Y, Frayo S, Convertine AJ, Margineantu D, Booth G et al. ( 2014 ) . A Computationally Designed Inhibitor of an Epstein-Barr Viral Bcl-2 Protein Induces Apoptosis in Infected Cells . Cell vol. 157 , ( 7 ) 1644 - 1656 .

Lopez-Ramirez MA, Wu D, Pryce G, Reijerkerk A, Kay O, de Vries HE, Hirst MC, Sharrack B ( 2014 ) . MicroRNA-155 negatively affects blood-brain barrier function during neuroinflammation . FASEB J vol. 28 , ( 6 ) 2551 - 2565 .

King NP, Bale JB, Sheffler W, McNamara DE, Gonen S, Gonen T, Yeates TO, Baker D ( 2014 ) . Accurate design of co-assembling multi-component protein nanomaterials . Nature vol. 510 , ( 7503 ) 103 - 108 .

Chen K-YM, Sun J, Salvo JS, Baker D, Barth P ( 2014 ) . High-Resolution Modeling of Transmembrane Helical Protein Structures from Distant Homologues . PLOS Computational Biology vol. 10 , ( 5 )

Preiswerk N, Beck T, Schulz JD, Milovník P, Mayer C, Siegel JB, Baker D, Hilvert D ( 2014 ) . Impact of scaffold rigidity on the design and evolution of an artificial Diels-Alderase . Proceedings of the National Academy of Sciences of the United States of America vol. 111 , ( 22 ) 8013 - 8018 .

King C, Garza EN, Mazor R, Linehan JL, Pastan I, Pepper M, Baker D ( 2014 ) . Removing T-cell epitopes with computational protein design . Proceedings of the National Academy of Sciences of the United States of America vol. 111 , ( 23 ) 8577 - 8582 .

Mazor R, Eberle JA, Hu X, Vassall AN, Onda M, Beers R, Lee EC, Kreitman RJ et al. ( 2014 ) . Recombinant immunotoxin for cancer treatment with low immunogenicity by identification and silencing of human T-cell epitopes . Proceedings of the National Academy of Sciences of the United States of America vol. 111 , ( 23 ) 8571 - 8576 .

Alushin GM, Lander GC, Kellogg EH, Zhang R, Baker D, Nogales E ( 2014 ) . High-Resolution Microtubule Structures Reveal the Structural Transitions in αβ-Tubulin upon GTP Hydrolysis . Cell vol. 157 , ( 5 ) 1117 - 1129 .

Ovchinnikov S, Kamisetty H, Baker D ( 2014 ) . Robust and accurate prediction of residue–residue interactions across protein interfaces using evolutionary information . eLife vol. 3 ,

Browne L, Lidster K, Clutterbuck L, Posada C, Chan AWE, Riddall D, Garthwaite J ( 2014 ) . Imidazol-1-ylethylindazole voltage-gated sodium channel ligands are neuroprotective during optic neuritis in a mouse model of multiple sclerosis . J Med Chem vol. 57 , ( 7 ) 2942 - 2952 .

Baker DJ, Richards G ( 2014 ) . On the delivery of weather services and parallels for the development of operational forest carbon measurement, reporting and verification systems . Carbon Management vol. 2 , ( 5 ) 567 - 573 .

Rajagopalan S, Wang C, Yu K, Kuzin AP, Richter F, Lew S, Miklos AE, Matthews ML et al. ( 2014 ) . Design of activated serine–containing catalytic triads with atomic-level accuracy . Nature Chemical Biology vol. 10 , ( 5 ) 386 - 391 .

Wang Y, Khan IF, Boissel S, Jarjour J, Pangallo J, Thyme S, Baker D, Scharenberg AM et al. ( 2014 ) . Progressive engineering of a homing endonuclease genome editing reagent for the murine X-linked immunodeficiency locus . Nucleic Acids Research vol. 42 , ( 10 ) 6463 - 6475 .

Baker D ( 2014 ) . Centenary Award and Sir Frederick Gowland Hopkins Memorial Lecture. Protein folding, structure prediction and design . Biochemical Society Transactions vol. 42 , ( 2 ) 225 - 229 .

Baker DJ, Atkinson AM, Wilkinson GP, Coope GJ ( 2014 ) . Characterization of the heterozygous glucokinase knockout mouse as a translational disease model for glucose control in type 2 diabetes . British Journal of Pharmacology vol. 171 , ( 7 ) 1629 - 1641 .

Baker DJ, Wilkinson GP, Atkinson AM, Charles AD ( 2014 ) . Chronic glucokinase activator treatment at clinically translatable exposures gives durable glucose lowering in two animal models of type 2 diabetes . British Journal of Pharmacology vol. 171 , ( 7 ) 1642 - 1654 .

Obexer R, Studer S, Giger L, Pinkas DM, Grütter MG, Baker D, Hilvert D ( 2014 ) . Active Site Plasticity of a Computationally Designed Retro‐Aldolase Enzyme . ChemCatChem vol. 6 , ( 4 ) 1043 - 1050 .

Puentes F, Topping J, Kuhle J, van der Star BJ, Douiri A, Giovannoni G, Baker D, Amor S et al. ( 2014 ) . Immune reactivity to neurofilament proteins in the clinical staging of amyotrophic lateral sclerosis . J Neurol Neurosurg Psychiatry vol. 85 , ( 3 ) 274 - 278 .

Correia BE, Bates JT, Loomis RJ, Baneyx G, Carrico C, Jardine JG, Rupert P, Correnti C et al. ( 2014 ) . Proof of principle for epitope-focused vaccine design . Nature vol. 507 , ( 7491 ) 201 - 206 .

Dua P, Warnes G, Chruch A, Baker D, Giovannoni G, Meier UC ( 2014 ) . Functional effects of anti-neuronal antibodies from patients with Tourette's syndrome and disorders associated with streptococcal infection . Neurology Psychiatry and Brain Research vol. 20 , ( 1 ) 17 - 18 .

Mao B, Tejero R, Baker D, Montelione GT ( 2014 ) . Protein NMR Structures Refined with Rosetta Have Higher Accuracy Relative to Corresponding X‑ray Crystal Structures . Journal of the American Chemical Society vol. 136 , ( 5 ) 1893 - 1906 .

Thyme S, Baker D ( 2014 ) . Redesigning the Specificity of Protein–DNA Interactions with Rosetta . Methods in Molecular Biology vol. 1123 , 265 - 282 .

Wijma HJ, Floor RJ, Jekel PA, Baker D, Marrink SJ, Janssen DB ( 2014 ) . Computationally designed libraries for rapid enzyme stabilization . Protein Engineering Design and Selection vol. 27 , ( 2 ) 49 - 58 .

Pakpoor J, Nyein S, Disanto G, Nwosu A, Baker D ( 2014 ) . A global analysis of the use of social media to discuss multiple sclerosis . MULTIPLE SCLEROSIS JOURNAL . vol. 20 , 334 - 335 .

Pryce G, Visintin C, Ramagopalan SV, Al-Izki S, De Faveri LE, Nuamah RA, Mein CA, Montpetit A et al. ( 2014 ) . Control of spasticity in a multiple sclerosis model using central nervous system-excluded CB1 cannabinoid receptor agonists . FASEB J vol. 28 , ( 1 ) 117 - 130 .

Baker D ( 2014 ) . Experimental autoimmune encephalomyelitis is a good model of multiple sclerosis if used wisely . Multiple Sclerosis and Related Disorders

Whyte L, Khalid A, Chiu S, Baker D ( 2014 ) . GPR55 Regulates Peak Bone Mass and Steroid Hormone Levels in Male Mice . JOURNAL OF BONE AND MINERAL RESEARCH . vol. 29 , S409 - S409 .

Liu B, Song S, Baker D, Hassan Z, Drynda RL, Bowe JE ( 2014 ) . GPR55 deletion is coupled to impaired insulin secretion and reduced islet cell turnover . DIABETIC MEDICINE vol. 31 , 9 - 9 .

Baker D, Pell C ( 2014 ) . HIV infection as a chronic disease: Optimising outcomes . Medicine Today vol. 15 , ( 2 ) 16 - 26 .

Amor S, Peferoen LAN, Vogel DYS, van der Valk P, Van Noort JM ( 2014 ) . Inflammation in neurodegenerative diseases - an update . Immunology vol. 142 , ( 2 ) 151 - 166 .

Liu B, Song S, Baker D, Hassan Z, Drynda RL, Persaud SJ ( 2014 ) . Knockout of GPR55 impairs insulin secretion and reduces islet cell turnover . DIABETOLOGIA vol. 57 , S49 - S49 .

Mullen L, Rigby A, Sclanders M, Adams G, Mittal G, Colston J, Fatah R, Subang C et al. ( 2014 ) . Latency can be conferred to a variety of cytokines by fusion with latency-associated peptide from TGF-β . Expert Opin Drug Deliv vol. 11 , ( 1 ) 5 - 16 .

Mullen L, Adams G, Layward L, Vessillier S, Annenkov A, Mittal G, Rigby A, Sclanders M et al. ( 2014 ) . Latent cytokines for targeted therapy of inflammatory disorders . Expert Opin Drug Deliv vol. 11 , ( 1 ) 101 - 110 .

Al-Izki S, Pryce G, Hankey DJR, Lidster K, von Kutzleben SM, Browne L, Clutterbuck L, Posada C et al. ( 2014 ) . Lesional-targeting of neuroprotection to the inflammatory penumbra in experimental multiple sclerosis . Brain vol. 137 , ( Pt 1 ) 92 - 108 .

Baker D, Pepper G, Yauner F ( 2014 ) . MSer - A new, neutral descriptor for someone with multiple sclerosis . Multiple Sclerosis and Related Disorders vol. 3 , ( 1 ) 31 - 33 .

Song S, Liu B, Bowe JE, Baker D ( 2014 ) . Specificity of GPR55 agonists and antagonist in the regulation of calcium handling and insulin secretion by mouse islets . DIABETIC MEDICINE vol. 31 , 32 - 32 .

Baker D, Lidster K, Sottomayor A ( 2014 ) . Two years later: journals are not yet enforcing the ARRIVE guidelines on reporting standards for pre-clinical animal studies . PLoS Biol vol. 12 , ( 1 )

Strauch E-M, Fleishman SJ, Baker D ( 2013 ) . Computational design of a pH-sensitive IgG binding protein . Proceedings of the National Academy of Sciences of the United States of America vol. 111 , ( 2 ) 675 - 680 .

Hampton DW, Serio A, Al-Izki S, Giovannoni G, Baker D ( 2013 ) . Neurodegeneration progresses despite complete elimination of clinical relapses in a mouse model of multiple sclerosis . Acta Neuropathologica Communications vol. 1 , ( 1 )

Fang J, Mehlich A, Koga N, Huang J, Koga R, Gao X, Hu C, Jin C et al. ( 2013 ) . Forced protein unfolding leads to highly elastic and tough protein hydrogels . Nature Communications vol. 4 , ( 1 )

Pryce G, Cabranes A, Fernández-Ruiz J, Bisogno T, Long JZ, Giovannoni G ( 2013 ) . Control of experimental spasticity by targeting the degradation of endocannabinoids using selective fatty acid amide hydrolase inhibitors . Mult Scler vol. 19 , ( 14 ) 1896 - 1904 .

Delarasse C, Smith P, Baker D ( 2013 ) . Novel pathogenic epitopes of myelin oligodendrocyte glycoprotein induce experimental autoimmune encephalomyelitis in C57BL/6 mice . Immunology vol. 140 , ( 4 ) 456 - 464 .

Boissel S, Jarjour J, Astrakhan A, Adey A, Gouble A, Duchateau P, Shendure J, Stoddard BL et al. ( 2013 ) . megaTALs: a rare-cleaving nuclease architecture for therapeutic genome engineering . Nucleic Acids Research vol. 42 , ( 4 ) 2591 - 2601 .

Nivón LG, Bjelic S, King C, Baker D ( 2013 ) . Automating human intuition for protein design . Proteins Structure Function and Bioinformatics vol. 82 , ( 5 ) 858 - 866 .

Conway P, Tyka MD, DiMaio F, Konerding DE, Baker D ( 2013 ) . Relaxation of backbone bond geometry improves protein energy landscape modeling . Protein Science vol. 23 , ( 1 ) 47 - 55 .

Thyme SB, Boissel SJS, Quadri SA, Nolan T, Baker DA, Park RU, Kusak L, Ashworth J et al. ( 2013 ) . Reprogramming homing endonuclease specificity through computational design and directed evolution . Nucleic Acids Research vol. 42 , ( 4 ) 2564 - 2576 .

Fishpool DT, Rezai A, Baker D, Ogin SL ( 2013 ) . Interlaminar toughness characterisation of 3D woven carbon fibre composites . Plastics, Rubber and Composites vol. 42 , ( 3 ) 108 - 114 .

Bjelic S, Kipnis Y, Wang L, Pianowski Z, Vorobiev S, Su M, Seetharaman J, Xiao R et al. ( 2013 ) . Exploration of Alternate Catalytic Mechanisms and Optimization Strategies for Retroaldolase Design . Journal of Molecular Biology vol. 426 , ( 1 ) 256 - 271 .

Wittenberg G, Sheffler W, Darchi D, Baker D, Noy D ( 2013 ) . Accelerated electron transport from photosystem I to redox partners by covalently linked ferredoxin . Physical Chemistry Chemical Physics vol. 15 , ( 45 ) 19608 - 19614 .

Cherny I, Greisen P, Ashani Y, Khare SD, Oberdorfer G, Leader H, Baker D, Tawfik DS ( 2013 ) . Engineering V‑Type Nerve Agents Detoxifying Enzymes Using Computationally Focused Libraries . ACS Chemical Biology vol. 8 , ( 11 ) 2394 - 2403 .

James E, Dobson R, Kuhle J, Baker D, Giovannoni G, Ramagopalan SV ( 2013 ) . The effect of vitamin D-related interventions on multiple sclerosis relapses: a meta-analysis . Mult Scler vol. 19 , ( 12 ) 1571 - 1579 .

DiMaio F, Echols N, Headd JJ, Terwilliger TC, Adams PD, Baker D ( 2013 ) . Improved low-resolution crystallographic refinement with Phenix and Rosetta . Nature Methods vol. 10 , ( 11 ) 1102 - 1104 .

Puentes F, van der Star BJ, Victor M, Kipp M, Ummenthum K, Pryce G, Gerritsen W, Huizinga R ( 2013 ) . Characterization of immune response to neurofilament light in experimental autoimmune encephalomyelitis . Journal of Neuroinflammation vol. 10 ,

Song Y, DiMaio F, Wang RY-R, Kim D, Miles C, Brunette T, Thompson J, Baker D ( 2013 ) . High-Resolution Comparative Modeling with RosettaCM . Structure vol. 21 , ( 10 ) 1735 - 1742 .

Kim DE, DiMaio F, Wang RY, Song Y, Baker D ( 2013 ) . One contact for every twelve residues allows robust and accurate topology‐level protein structure modeling . Proteins Structure Function and Bioinformatics vol. 82 , ( S2 ) 208 - 218 .

Kamisetty H, Ovchinnikov S, Baker D ( 2013 ) . Assessing the utility of coevolution-based residue–residue contact predictions in a sequence- and structure-rich era . Proceedings of the National Academy of Sciences of the United States of America vol. 110 , ( 39 ) 15674 - 15679 .

Tinberg CE, Khare SD, Dou J, Doyle L, Nelson JW, Schena A, Jankowski W, Kalodimos CG et al. ( 2013 ) . Computational design of ligand-binding proteins with high affinity and selectivity . Nature vol. 501 , ( 7466 ) 212 - 216 .

Cooper S, Khatib F, Baker D ( 2013 ) . Increasing Public Involvement in Structural Biology . Structure vol. 21 , ( 9 ) 1482 - 1484 .

Shropshire TD, Reifert J, Rajagopalan S, Baker D, Feinstein SC, Daugherty PS ( 2013 ) . Amyloid β peptide cleavage by kallikrein 7 attenuates fibril growth and rescues neurons from Aβ-mediated toxicity in vitro . Biological Chemistry vol. 395 , ( 1 ) 109 - 118 .

Mills JH, Khare SD, Bolduc JM, Forouhar F, Mulligan VK, Lew S, Seetharaman J, Tong L et al. ( 2013 ) . Computational Design of an Unnatural Amino Acid Dependent Metalloprotein with Atomic Level Accuracy . Journal of the American Chemical Society vol. 135 , ( 36 ) 13393 - 13399 .

Richter F, Baker D ( 2013 ) . Computational Protein Design for Synthetic Biology . Synthetic Biology ,

Moretti R, Fleishman SJ, Agius R, Torchala M, Bates PA, Kastritis PL, Rodrigues JPGLM, Trellet M et al. ( 2013 ) . Community‐wide evaluation of methods for predicting the effect of mutations on protein–protein interactions . Proteins Structure Function and Bioinformatics vol. 81 , ( 11 ) 1980 - 1987 .

Vernon R, Shen Y, Baker D, Lange OF ( 2013 ) . Improved chemical shift based fragment selection for CS-Rosetta using Rosetta3 fragment picker . Journal of Biomolecular NMR vol. 57 , ( 2 ) 117 - 127 .

van der Schot G, Zhang Z, Vernon R, Shen Y, Vranken WF, Baker D, Bonvin AMJJ, Lange OF ( 2013 ) . Improving 3D structure prediction from chemical shift data . Journal of Biomolecular NMR vol. 57 , ( 1 ) 27 - 35 .

Moal IH, Moretti R, Baker D, Fernández-Recio J ( 2013 ) . Scoring functions for protein–protein interactions . Current Opinion in Structural Biology vol. 23 , ( 6 ) 862 - 867 .

Procko E, Hedman R, Hamilton K, Seetharaman J, Fleishman SJ, Su M, Aramini J, Kornhaber G et al. ( 2013 ) . Computational Design of a Protein-Based Enzyme Inhibitor . Journal of Molecular Biology vol. 425 , ( 18 ) 3563 - 3575 .

Giger L, Caner S, Obexer R, Kast P, Baker D, Ban N, Hilvert D ( 2013 ) . Evolution of a designed retro-aldolase leads to complete active site remodeling . Nature Chemical Biology vol. 9 , ( 8 ) 494 - 498 .

DiMaio F, Zhang J, Chiu W, Baker D ( 2013 ) . Cryo‐EM model validation using independent map reconstructions . Protein Science vol. 22 , ( 6 ) 865 - 868 .

Richter F, Baker D ( 2013 ) . Computational protein design for synthetic biology . Synthetic Biology Tools and Applications ,

Bergeron JRC, Worrall LJ, Sgourakis NG, DiMaio F, Pfuetzner RA, Felise HB, Vuckovic M, Yu AC et al. ( 2013 ) . A Refined Model of the Prototypical Salmonella SPI-1 T3SS Basal Body Reveals the Molecular Basis for Its Assembly . PLOS Pathogens vol. 9 , ( 4 )

Nivón LG, Moretti R, Baker D ( 2013 ) . A Pareto-Optimal Refinement Method for Protein Design Scaffolds . PLOS ONE vol. 8 , ( 4 )

Jardine J, Julien J-P, Menis S, Ota T, Kalyuzhniy O, McGuire A, Sok D, Huang P-S et al. ( 2013 ) . Rational HIV Immunogen Design to Target Specific Germline B Cell Receptors . Science vol. 340 , ( 6133 ) 711 - 716 .

Kiss G, Çelebi‐Ölçüm N, Moretti R, Baker D, Houk KN ( 2013 ) . Computational Enzyme Design . Angewandte Chemie International Edition vol. 52 , ( 22 ) 5700 - 5725 .

Demers J-P, Sgourakis NG, Gupta R, Loquet A, Giller K, Riedel D, Laube B, Kolbe M et al. ( 2013 ) . The Common Structural Architecture of Shigella flexneri and Salmonella typhimurium Type Three Secretion Needles . PLOS Pathogens vol. 9 , ( 3 )

Adams PD, Baker D, Brunger AT, Das R, DiMaio F, Read RJ, Richardson DC, Richardson JS et al. ( 2013 ) . Advances, Interactions, and Future Developments in the CNS, Phenix, and Rosetta Structural Biology Software Systems . Annual Review of Biophysics vol. 42 , ( 1 ) 265 - 287 .

Bjelic S, Nivón LG, Çelebi-Ölçüm N, Kiss G, Rosewall CF, Lovick HM, Ingalls EL, Gallaher JL et al. ( 2013 ) . Computational Design of Enone-Binding Proteins with Catalytic Activity for the Morita–Baylis–Hillman Reaction . ACS Chemical Biology vol. 8 , ( 4 ) 749 - 757 .

Baker D, Lidster K, Al-Izki S, Pryce G ( 2013 ) . Animal models of progressive disability in MS . IRISH JOURNAL OF MEDICAL SCIENCE vol. 182 , S5 - S6 .

Whitehead TA, Baker D, Fleishman SJ ( 2013 ) . Computational design of novel protein binders and experimental affinity maturation . Methods in Enzymology , vol. 523 ,

Di Filippo M, Chiasserini D, Gardoni F, Viviani B, Tozzi A, Giampa C, Costa C, Tantucci M et al. ( 2013 ) . Effects of central and peripheral inflammation on hippocampal synaptic plasticity . NEUROBIOLOGY OF DISEASE vol. 52 , 229 - 236 .

Liu B, Song S, Baker D, Bowe J, Hassan Z ( 2013 ) . GPR55 deletion is coupled to impaired glucose tolerance and increased islet cell apoptosis . DIABETOLOGIA . vol. 56 , S46 - S46 .

Sisay S, Pryce G, Jackson SJ, Tanner C, Ross RA, Michael GJ ( 2013 ) . Genetic background can result in a marked or minimal effect of gene knockout (GPR55 and CB2 receptor) in experimental autoimmune encephalomyelitis models of multiple sclerosis . PLoS One vol. 8 , ( 10 )

Baker D, Pepper G ( 2013 ) . MSer - A new, neutral descriptor for someone with multiple sclerosis . Multiple Sclerosis and Related Disorders

Lidster K, Jackson SJ, Ahmed Z, Munro P, Coffey P, Baker MD ( 2013 ) . Neuroprotection in a novel mouse model of multiple sclerosis . PLoS One vol. 8 , ( 11 )

Molski MA, Goodman JL, Chou F-C, Baker D, Das R, Schepartz A ( 2013 ) . Remodeling a β- peptide bundle . Chemical Science vol. 4 , ( 1 ) 319 - 324 .

Leaver-Fay A, O'Meara MJ, Tyka M, Jacak R, Song Y, Kellogg EH, Thompson J, Davis IW et al. ( 2013 ) . Scientific benchmarks for guiding macromolecular energy function improvement . Methods in Enzymology , vol. 523 ,

Khoury GA, Liwo A, Khatib F, Zhou H, Chopra G, Bacardit J, Bortot LO, Faccioli RA et al. ( 2013 ) . Wefold: A collaborative protein structure prediction experiment . Computational Molecular Science and Engineering Forum 2013 Core Programming Area at the 2013 Aiche Annual Meeting Global Challenges for Engineering A Sustainable Future . 182 - 184 .

Baker DJ ( 2012 ) . Cloudy Forecast for Weather Satellite Data . Science vol. 338 , ( 6113 ) 1419 - 1419 .

Baker D, Lidster K, Sottomayor A ( 2012 ) . Reproducibility: Research-reporting standards fall short . Nature vol. 492 , ( 7427 )

Gordon SR, Stanley EJ, Wolf S, Toland A, Wu SJ, Hadidi D, Mills JH, Baker D et al. ( 2012 ) . Computational Design of an α‑Gliadin Peptidase . Journal of the American Chemical Society vol. 134 , ( 50 ) 20513 - 20520 .

Baker D, Lidster K, Amor S ( 2012 ) . Research-reporting standards fall short . Nature vol. 492 , ( 7427 ) 41 - 41 .

Koga N, Tatsumi-Koga R, Liu G, Xiao R, Acton TB, Montelione GT, Baker D ( 2012 ) . Principles for designing ideal protein structures . Nature vol. 491 , ( 7423 ) 222 - 227 .

Wu W, Ahlsen G, Baker D, Shapiro L, Zipursky SL ( 2012 ) . Complementary Chimeric Isoforms Reveal Dscam1 Binding Specificity In Vivo . Neuron vol. 76 , ( 3 )

Malich G, Coupland R, Donnelly S ( 2012 ) . A proposal for field-level medical assistance in an international humanitarian response to chemical, biological, radiological or nuclear events . Emergency Medicine Journal vol. 30 , ( 10 )

Harger M, Zheng L, Moon A, Ager C, An JH, Choe C, Lai Y-L, Mo B et al. ( 2012 ) . Expanding the Product Profile of a Microbial Alkane Biosynthetic Pathway . ACS Synthetic Biology vol. 2 , ( 1 ) 59 - 62 .

Richter F, Blomberg R, Khare SD, Kiss G, Kuzin AP, Smith AJT, Gallaher J, Pianowski Z et al. ( 2012 ) . Computational Design of Catalytic Dyads and Oxyanion Holes for Ester Hydrolysis . Journal of the American Chemical Society vol. 134 , ( 39 ) 16197 - 16206 .

Kellogg EH, Lange OF, Baker D ( 2012 ) . Evaluation and Optimization of Discrete State Models of Protein Folding . The Journal of Physical Chemistry B vol. 116 , ( 37 ) 11405 - 11413 .

Kipnis Y, Baker D ( 2012 ) . Comparison of designed and randomly generated catalysts for simple chemical reactions . Protein Science vol. 21 , ( 9 ) 1388 - 1395 .

Loquet A, Sgourakis NG, Gupta R, Giller K, Riedel D, Goosmann C, Griesinger C, Kolbe M et al. ( 2012 ) . Correction: Corrigendum: Atomic model of the type III secretion system needle . Nature vol. 488 , ( 7413 ) 684 - 684 .

Baker D ( 2012 ) . Multiple sclerosis - from bench to bedside . CNS Neurol Disord Drug Targets vol. 11 , ( 5 ) 495 - 496 .

Lidster K ( 2012 ) . Optical coherence tomography detection of neurodegeneration in multiple sclerosis . CNS Neurol Disord Drug Targets vol. 11 , ( 5 ) 518 - 527 .

Pryce G ( 2012 ) . Potential control of multiple sclerosis by cannabis and the endocannabinoid system . CNS Neurol Disord Drug Targets vol. 11 , ( 5 ) 624 - 641 .

Tyka MD, Jung K, Baker D ( 2012 ) . Efficient sampling of protein conformational space using fast loop building and batch minimization on highly parallel computers . Journal of Computational Chemistry vol. 33 , ( 31 ) 2483 - 2491 .

Alon A, Grossman I, Gat Y, Kodali VK, DiMaio F, Mehlman T, Haran G, Baker D et al. ( 2012 ) . The dynamic disulphide relay of quiescin sulphydryl oxidase . Nature vol. 488 , ( 7411 ) 414 - 418 .

Amor S, Baker D ( 2012 ) . Checklist for reporting and reviewing studies of experimental animal models of multiple sclerosis and related disorders . Multiple Sclerosis and Related Disorders vol. 1 , ( 3 ) 111 - 115 .

Baker D ( 2012 ) . Civilian Exposure to Toxic Agents: Emergency Medical Response . Prehospital and Disaster Medicine vol. 19 , ( 2 ) 174 - 178 .

Baker D ( 2012 ) . Improving Decontamination Procedures: A Priority for Chemical Incident Management . Prehospital and Disaster Medicine vol. 25 , ( 5 ) 440 - 441 .

Lange OF, Rossi P, Sgourakis NG, Song Y, Lee H-W, Aramini JM, Ertekin A, Xiao R et al. ( 2012 ) . Determination of solution structures of proteins up to 40 kDa using CS-Rosetta with sparse NMR data from deuterated samples . Proceedings of the National Academy of Sciences of the United States of America vol. 109 , ( 27 ) 10873 - 10878 .

Khersonsky O, Kiss G, Röthlisberger D, Dym O, Albeck S, Houk KN, Baker D, Tawfik DS ( 2012 ) . Bridging the gaps in design methodologies by evolutionary optimization of the stability and proficiency of designed Kemp eliminase KE59 . Proceedings of the National Academy of Sciences of the United States of America vol. 109 , ( 26 ) 10358 - 10363 .

Baxter S, Lambert AR, Kuhar R, Jarjour J, Kulshina N, Parmeggiani F, Danaher P, Gano J et al. ( 2012 ) . Engineering domain fusion chimeras from I-OnuI family LAGLIDADG homing endonucleases . Nucleic Acids Research vol. 40 , ( 16 ) 7985 - 8000 .

Thompson JM, Sgourakis NG, Liu G, Rossi P, Tang Y, Mills JL, Szyperski T, Montelione GT et al. ( 2012 ) . Accurate protein structure modeling using sparse NMR data and homologous structure information . Proceedings of the National Academy of Sciences of the United States of America vol. 109 , ( 25 ) 9875 - 9880 .

King NP, Sheffler W, Sawaya MR, Vollmar BS, Sumida JP, André I, Gonen T, Yeates TO et al. ( 2012 ) . Computational Design of Self-Assembling Protein Nanomaterials with Atomic Level Accuracy . Science vol. 336 , ( 6085 ) 1171 - 1174 .

Gnanapavan S, Grant D, Pryce G, Baker D ( 2012 ) . Neurofilament a biomarker of neurodegeneration in autoimmune encephalomyelitis . Autoimmunity vol. 45 , ( 4 ) 298 - 303 .

Whitehead TA, Chevalier A, Song Y, Dreyfus C, Fleishman SJ, De Mattos C, Myers CA, Kamisetty H et al. ( 2012 ) . Optimization of affinity, specificity and function of designed influenza inhibitors using deep sequencing . Nature Biotechnology vol. 30 , ( 6 ) 543 - 548 .

Loquet A, Sgourakis NG, Gupta R, Giller K, Riedel D, Goosmann C, Griesinger C, Kolbe M et al. ( 2012 ) . Atomic model of the type III secretion system needle . Nature vol. 486 , ( 7402 ) 276 - 279 .

Morin A, Urban J, Adams PD, Foster I, Sali A, Baker D, Sliz P ( 2012 ) . Shining Light into Black Boxes . Science vol. 336 , ( 6078 ) 159 - 160 .

Wu W, Ahlsen G, Baker D, Shapiro L, Zipursky SL ( 2012 ) . Complementary Chimeric Isoforms Reveal Dscam1 Binding Specificity In Vivo . Neuron vol. 74 , ( 2 ) 261 - 268 .

Fleishman SJ, Baker D ( 2012 ) . Role of the Biomolecular Energy Gap in Protein Design, Structure, and Evolution . Cell vol. 149 , ( 2 ) 262 - 273 .

Baker D, Pryce G, Jackson SJ ( 2012 ) . The biology that underpins the therapeutic potential of cannabis-based medicines for the control of spasticity in multiple sclerosis . Multiple Sclerosis and Related Disorders vol. 1 , ( 2 ) 64 - 75 .

Althoff EA, Wang L, Jiang L, Giger L, Lassila JK, Wang Z, Smith M, Hari S et al. ( 2012 ) . Robust design and optimization of retroaldol enzymes . Protein Science vol. 21 , ( 5 ) 717 - 726 .

Thyme SB, Baker D, Bradley P ( 2012 ) . Improved Modeling of Side-Chain–Base Interactions and Plasticity in Protein–DNA Interface Design . Journal of Molecular Biology vol. 419 , ( 3-4 ) 255 - 274 .

Terwilliger TC, DiMaio F, Read RJ, Baker D, Bunkóczi G, Adams PD, Grosse-Kunstleve RW, Afonine PV et al. ( 2012 ) . phenix.mr_rosetta: molecular replacement and model rebuilding with Phenix and Rosetta . Journal of Structural and Functional Genomics vol. 13 , ( 2 ) 81 - 90 .

Khatib F, DiMaio F, Cooper S, Kazmierczyk M, Gilski M, Krzywda S, Zabranska H, Pichova I et al. ( 2012 ) . Erratum: Crystal structure of a monomeric retroviral protease solved by protein folding game players . Nature Structural & Molecular Biology vol. 19 , ( 3 ) 364 - 364 .

Dua P, Meier UC, Baker D, Giovannoni G ( 2012 ) . Functional effects of anti-neuronal antibodies in patients with encephalitis lethargica and other related disorders associated with streptococcal infection . Neurology Psychiatry and Brain Research vol. 18 , ( 2 )

Krzysiak TC, Jung J, Thompson J, Baker D, Gronenborn AM ( 2012 ) . APOBEC2 Is a Monomer in Solution: Implications for APOBEC3G Models . Biochemistry vol. 51 , ( 9 ) 2008 - 2017 .

Khare SD, Kipnis Y, Greisen PJ, Takeuchi R, Ashani Y, Goldsmith M, Song Y, Gallaher JL et al. ( 2012 ) . Computational redesign of a mononuclear zinc metalloenzyme for organophosphate hydrolysis . Nature Chemical Biology vol. 8 , ( 3 ) 294 - 300 .

Rosato A, Aramini JM, Arrowsmith C, Bagaria A, Baker D, Cavalli A, Doreleijers JF, Eletsky A et al. ( 2012 ) . Blind Testing of Routine, Fully Automated Determination of Protein Structures from NMR Data . Structure vol. 20 , ( 2 ) 227 - 236 .

Wojdyla JA, Fleishman SJ, Baker D, Kleanthous C ( 2012 ) . Structure of the Ultra-High-Affinity Colicin E2 DNase–Im2 Complex . Journal of Molecular Biology vol. 417 , ( 1-2 ) 79 - 94 .

Eiben CB, Siegel JB, Bale JB, Cooper S, Khatib F, Shen BW, Players F, Stoddard BL et al. ( 2012 ) . Increased Diels-Alderase activity through backbone remodeling guided by Foldit players . Nature Biotechnology vol. 30 , ( 2 ) 190 - 192 .

Wargacki AJ, Leonard E, Win MN, Regitsky DD, Santos CNS, Kim PB, Cooper SR, Raisner RM et al. ( 2012 ) . An Engineered Microbial Platform for Direct Biofuel Production from Brown Macroalgae . Science vol. 335 , ( 6066 ) 308 - 313 .

Schmitz C, Vernon R, Otting G, Baker D, Huber T ( 2012 ) . Protein Structure Determination from Pseudocontact Shifts Using ROSETTA . Journal of Molecular Biology vol. 416 , ( 5 ) 668 - 677 .

Baker D, Amor S ( 2012 ) . Publication guidelines for refereeing and reporting on animal use in experimental autoimmune encephalomyelitis . J Neuroimmunol vol. 242 , ( 1-2 ) 78 - 83 .

van der Star BJ, Vogel DYS, Kipp M, Puentes F, Baker D ( 2012 ) . <i>In Vitro</i> and <i>In Vivo</i> Models of Multiple Sclerosis . CNS & NEUROLOGICAL DISORDERS-DRUG TARGETS vol. 11 , ( 5 ) 570 - 588 .

Lopez-Ramirez MA, Wu D, Pryce G, Simpson JE, Reijerkerk A, King-Robson J, de Vries HE, Sharrack B et al. ( 2012 ) . Endothelial miR-155 promotes blood brain barrier dysfunction in neuroinflammation . JOURNAL OF NEUROIMMUNOLOGY . vol. 253 , 3 - 4 .

Kipp M, Van Der Star B, Vogel DYS, Puentes F ( 2012 ) . Experimental in vivo and in vitro models of multiple sclerosis: EAE and beyond . Multiple Sclerosis and Related Disorders vol. 1 , ( 1 ) 15 - 28 .

Sher F, Amor S, Gerritsen W, Baker D, Boddeke E ( 2012 ) . Intraventricularly Injected Olig2-NSCs Attenuate Established Relapsing-Remitting EAE in Mice . CELL TRANSPLANTATION vol. 21 , ( 9 ) 1883 - 1897 .

Song S, Liu B, Baker D, Huang GC, Amiel SA, Bowe JE ( 2012 ) . Islet GPR55 is coupled to increased insulin secretion and decreased apoptosis . DIABETOLOGIA vol. 55 , S163 - S163 .

van Noort JM, Baker D ( 2012 ) . Mechanisms in the Development of Multiple Sclerosis Lesions: Reconciling Autoimmune and Neurodegenerative Factors . CNS & NEUROLOGICAL DISORDERS-DRUG TARGETS vol. 11 , ( 5 ) 556 - 569 .

van der Star B, Puentes F, Gerritsen W, Huizinga R, Reijerkerk A, van der Valk P ( 2012 ) . Neuronal specific T cells are pathogenic in Biozzi mice - Implications for MS . JOURNAL OF NEUROIMMUNOLOGY . vol. 253 , 155 - 155 .

Li C, Bowe JE, Baker D, Jones PM ( 2012 ) . PS 014 Beta cell GPCRs and other signalling mechanisms . DIABETOLOGIA vol. 55 , S163 - S163 .

Al-Izki S, O'Neill JK, Butter C, Giovannoni G, Amor S ( 2012 ) . Practical guide to the induction of relapsing progressive experimental autoimmune encephalomyelitis in the Biozzi ABH mouse . Multiple Sclerosis and Related Disorders vol. 1 , ( 1 ) 29 - 38 .

Fox RJ, Thompson A, Baker D, Baneke P, Brown D, Browne P, Chandraratna D, Ciccarelli O et al. ( 2012 ) . Setting a research agenda for progressive multiple sclerosis: The International Collaborative on Progressive MS . MULTIPLE SCLEROSIS JOURNAL vol. 18 , ( 11 ) 1534 - 1540 .

Lange OF, Baker D ( 2011 ) . Resolution‐adapted recombination of structural features significantly improves sampling in restraint‐guided structure calculation . Proteins Structure Function and Bioinformatics vol. 80 , ( 3 ) 884 - 895 .

Yarov-Yarovoy V, DeCaen PG, Westenbroek RE, Pan C-Y, Scheuer T, Baker D, Catterall WA ( 2011 ) . Structural basis for gating charge movement in the voltage sensor of a sodium channel . Proceedings of the National Academy of Sciences of the United States of America vol. 109 , ( 2 ) e93 - e102 .

Brzovic PS, Heikaus CC, Kisselev L, Vernon R, Herbig E, Pacheco D, Warfield L, Littlefield P et al. ( 2011 ) . The Acidic Transcription Activator Gcn4 Binds the Mediator Subunit Gal11/Med15 Using a Simple Protein Interface Forming a Fuzzy Complex . Molecular Cell vol. 44 , ( 6 ) 942 - 953 .

Handl J, Knowles J, Vernon R, Baker D, Lovell SC ( 2011 ) . The dual role of fragments in fragment‐assembly methods for de novo protein structure prediction . Proteins Structure Function and Bioinformatics vol. 80 , ( 2 ) 490 - 504 .

Khatib F, Cooper S, Tyka MD, Xu K, Makedon I, Popović Z, Baker D, Players F ( 2011 ) . Algorithm discovery by protein folding game players . Proceedings of the National Academy of Sciences of the United States of America vol. 108 , ( 47 ) 18949 - 18953 .

Wang L, Althoff EA, Bolduc J, Jiang L, Moody J, Lassila JK, Giger L, Hilvert D et al. ( 2011 ) . Structural Analyses of Covalent Enzyme–Substrate Analog Complexes Reveal Strengths and Limitations of De Novo Enzyme Design . Journal of Molecular Biology vol. 415 , ( 3 ) 615 - 625 .

Azoitei ML, Ban Y-EA, Julien J-P, Bryson S, Schroeter A, Kalyuzhniy O, Porter JR, Adachi Y et al. ( 2011 ) . Computational Design of High-Affinity Epitope Scaffolds by Backbone Grafting of a Linear Epitope . Journal of Molecular Biology vol. 415 , ( 1 ) 175 - 192 .

Azoitei ML, Correia BE, Ban Y-EA, Carrico C, Kalyuzhniy O, Chen L, Schroeter A, Huang P-S et al. ( 2011 ) . Computation-Guided Backbone Grafting of a Discontinuous Motif onto a Protein Scaffold . Science vol. 334 , ( 6054 ) 373 - 376 .

Gilski M, Kazmierczyk M, Krzywda S, Zábranská H, Cooper S, Popović Z, Khatib F, DiMaio F et al. ( 2011 ) . High-resolution structure of a retroviral protease folded as a monomer . Acta Crystallographica Section D, Structural Biology vol. 67 , ( 11 ) 907 - 914 .

Fleishman SJ, Whitehead TA, Strauch E-M, Corn JE, Qin S, Zhou H-X, Mitchell JC, Demerdash ONA et al. ( 2011 ) . Community-Wide Assessment of Protein-Interface Modeling Suggests Improvements to Design Methodology . Journal of Molecular Biology vol. 414 , ( 2 ) 289 - 302 .

Khatib F, DiMaio F, Cooper S, Kazmierczyk M, Gilski M, Krzywda S, Zabranska H, Pichova I et al. ( 2011 ) . Crystal structure of a monomeric retroviral protease solved by protein folding game players . Nature Structural & Molecular Biology vol. 18 , ( 10 ) 1175 - 1177 .

Fleishman SJ, Corn JE, Strauch E-M, Whitehead TA, Karanicolas J, Baker D ( 2011 ) . Hotspot-Centric De Novo Design of Protein Binders . Journal of Molecular Biology vol. 413 , ( 5 ) 1047 - 1062 .

Ayoub SS, Pryce G, Seed MP, Bolton C, Flower RJ ( 2011 ) . Paracetamol-induced hypothermia is independent of cannabinoids and transient receptor potential vanilloid-1 and is not mediated by AM404 . Drug Metab Dispos vol. 39 , ( 9 ) 1689 - 1695 .

Huang P-S, Ban Y-EA, Richter F, Andre I, Vernon R, Schief WR, Baker D ( 2011 ) . RosettaRemodel: A Generalized Framework for Flexible Backbone Protein Design . PLOS ONE vol. 6 , ( 8 )

Gront D, Kulp DW, Vernon RM, Strauss CEM, Baker D ( 2011 ) . Generalized Fragment Picking in Rosetta: Design, Protocols and Applications . PLOS ONE vol. 6 , ( 8 )

Saha P, Barua B, Bhattacharyya S, Balamurali MM, Schief WR, Baker D, Varadarajan R ( 2011 ) . Design and Characterization of Stabilized Derivatives of Human CD4D12 and CD4D1 . Biochemistry vol. 50 , ( 37 ) 7891 - 7900 .

Valkov E, Stamp A, DiMaio F, Baker D, Verstak B, Roversi P, Kellie S, Sweet MJ et al. ( 2011 ) . Crystal structure of Toll-like receptor adaptor MAL/TIRAP reveals the molecular basis for signal transduction and disease protection . Proceedings of the National Academy of Sciences of the United States of America vol. 108 , ( 36 ) 14879 - 14884 .

Bouvignies G, Vallurupalli P, Hansen DF, Correia BE, Lange O, Bah A, Vernon RM, Dahlquist FW et al. ( 2011 ) . Solution structure of a minor and transiently formed state of a T4 lysozyme mutant . Nature vol. 477 , ( 7362 ) 111 - 114 .

Al-Izki S, Pryce G, Jackson SJ ( 2011 ) . Immunosuppression with FTY720 is insufficient to prevent secondary progressive neurodegeneration in experimental autoimmune encephalomyelitis . Mult Scler vol. 17 , ( 8 ) 939 - 948 .

Wang RY-R, Han Y, Krassovsky K, Sheffler W, Tyka M, Baker D ( 2011 ) . Modeling Disordered Regions in Proteins Using Rosetta . PLOS ONE vol. 6 , ( 7 )

Szeto MD, Boissel SJS, Baker D, Thyme SB ( 2011 ) . Mining Endonuclease Cleavage Determinants in Genomic Sequence Data* . Journal of Biological Chemistry vol. 286 , ( 37 ) 32617 - 32627 .

Wu SJ, Eiben CB, Carra JH, Huang I, Zong D, Liu P, Wu CT, Nivala J et al. ( 2011 ) . Improvement of a Potential Anthrax Therapeutic by Computational Protein Design* . Journal of Biological Chemistry vol. 286 , ( 37 ) 32586 - 32592 .

Jackson SJ, Giovannoni G ( 2011 ) . Fingolimod modulates microglial activation to augment markers of remyelination . J Neuroinflammation vol. 8 ,

Cooper S, Khatib F, Makedon I, Lu H, Barbero J, Baker D, Fogarty J, Popović Z et al. ( 2011 ) . Analysis of social gameplay macros in the Foldit cookbook . Conference: Proceedings of the 6th International Conference on Foundations of Digital Games9 - 14 .

Korzhnev DM, Vernon RM, Religa TL, Hansen AL, Baker D, Fersht AR, Kay LE ( 2011 ) . Nonnative Interactions in the FF Domain Folding Pathway from an Atomic Resolution Structure of a Sparsely Populated Intermediate: An NMR Relaxation Dispersion Study . Journal of the American Chemical Society vol. 133 , ( 28 ) 10974 - 10982 .

Fleishman SJ, Leaver-Fay A, Corn JE, Strauch E-M, Khare SD, Koga N, Ashworth J, Murphy P et al. ( 2011 ) . RosettaScripts: A Scripting Language Interface to the Rosetta Macromolecular Modeling Suite . PLOS ONE vol. 6 , ( 6 )

DiMaio F, Leaver-Fay A, Bradley P, Baker D, André I ( 2011 ) . Modeling Symmetric Macromolecular Structures in Rosetta3 . PLOS ONE vol. 6 , ( 6 )

Sievers SA, Karanicolas J, Chang HW, Zhao A, Jiang L, Zirafi O, Stevens JT, Münch J et al. ( 2011 ) . Structure-based design of non-natural amino-acid inhibitors of amyloid fibril formation . Nature vol. 475 , ( 7354 ) 96 - 100 .

Thompson J, Baker D ( 2011 ) . Incorporation of evolutionary information into Rosetta comparative modeling . Proteins Structure Function and Bioinformatics vol. 79 , ( 8 ) 2380 - 2388 .

Baker D, Gerritsen W, Amor S ( 2011 ) . Critical appraisal of animal models of multiple sclerosis . Mult Scler vol. 17 , ( 6 ) 647 - 657 .

Warner LR, Varga K, Lange OF, Baker SL, Baker D, Sousa MC, Pardi A ( 2011 ) . Structure of the BamC Two-Domain Protein Obtained by Rosetta with a Limited NMR Data Set . Journal of Molecular Biology vol. 411 , ( 1 ) 83 - 95 .

Richter F, Leaver-Fay A, Khare SD, Bjelic S, Baker D ( 2011 ) . De Novo Enzyme Design Using Rosetta3 . PLOS ONE vol. 6 , ( 5 )

Fleishman SJ, Whitehead TA, Ekiert DC, Dreyfus C, Corn JE, Strauch E-M, Wilson IA, Baker D ( 2011 ) . Computational Design of Proteins Targeting the Conserved Stem Region of Influenza Hemagglutinin . Science vol. 332 , ( 6031 ) 816 - 821 .

Zhang J, Ma B, DiMaio F, Douglas NR, Joachimiak LA, Baker D, Frydman J, Levitt M et al. ( 2011 ) . Cryo-EM Structure of a Group II Chaperonin in the Prehydrolysis ATP-Bound State Leading to Lid Closure . Structure vol. 19 , ( 5 ) 633 - 639 .

DiMaio F, Terwilliger TC, Read RJ, Wlodawer A, Oberdorfer G, Wagner U, Valkov E, Alon A et al. ( 2011 ) . Improved molecular replacement by density- and energy-guided protein structure optimization . Nature vol. 473 , ( 7348 ) 540 - 543 .

Lyskowski A, Oeemig JS, Jaakkonen A, Rommi K, DiMaio F, Zhou D, Kajander T, Baker D et al. ( 2011 ) . Cloning, expression, purification, crystallization and preliminary X-ray diffraction data of the Pyrococcus horikoshii RadA intein . Acta Crystallographica Section F: Structural Biology Communications vol. 67 , ( 5 ) 623 - 626 .

Windbichler N, Menichelli M, Papathanos PA, Thyme SB, Li H, Ulge UY, Hovde BT, Baker D et al. ( 2011 ) . A synthetic homing endonuclease-based gene drive system in the human malaria mosquito . Nature vol. 473 , ( 7346 ) 212 - 215 .

Song Y, Tyka M, Leaver‐Fay A, Thompson J, Baker D ( 2011 ) . Structure‐guided forcefield optimization . Proteins Structure Function and Bioinformatics vol. 79 , ( 6 ) 1898 - 1909 .

Sgourakis NG, Lange OF, DiMaio F, André I, Fitzkee NC, Rossi P, Montelione GT, Bax A et al. ( 2011 ) . Determination of the Structures of Symmetric Protein Oligomers from NMR Chemical Shifts and Residual Dipolar Couplings . Journal of the American Chemical Society vol. 133 , ( 16 ) 6288 - 6298 .

Karanicolas J, Corn JE, Chen I, Joachimiak LA, Dym O, Peck SH, Albeck S, Unger T et al. ( 2011 ) . A De Novo Protein Binding Pair By Computational Design and Directed Evolution . Molecular Cell vol. 42 , ( 2 ) 250 - 260 .

Fleishman SJ, Khare SD, Koga N, Baker D ( 2011 ) . Restricted sidechain plasticity in the structures of native proteins and complexes . Protein Science vol. 20 , ( 4 ) 753 - 757 .

Ulge UY, Baker DA, Monnat RJ ( 2011 ) . Comprehensive computational design of mCreI homing endonuclease cleavage specificity for genome engineering . Nucleic Acids Research vol. 39 , ( 10 ) 4330 - 4339 .

Khersonsky O, Röthlisberger D, Wollacott AM, Murphy P, Dym O, Albeck S, Kiss G, Houk KN et al. ( 2011 ) . Optimization of the In-Silico-Designed Kemp Eliminase KE70 by Computational Design and Directed Evolution . Journal of Molecular Biology vol. 407 , ( 3 ) 391 - 412 .

Guenaga J, Dosenovic P, Ofek G, Baker D, Schief WR, Kwong PD, Hedestam GBK, Wyatt RT ( 2011 ) . Heterologous Epitope-Scaffold Prime∶Boosting Immuno-Focuses B Cell Responses to the HIV-1 gp41 2F5 Neutralization Determinant . PLOS ONE vol. 6 , ( 1 )

Li M, DiMaio F, Zhou D, Gustchina A, Lubkowski J, Dauter Z, Baker D, Wlodawer A ( 2011 ) . Crystal structure of XMRV protease differs from the structures of other retropepsins . Nature Structural & Molecular Biology vol. 18 , ( 2 ) 227 - 229 .

Chen D-H, Baker ML, Hryc CF, DiMaio F, Jakana J, Wu W, Dougherty M, Haase-Pettingell C et al. ( 2011 ) . Structural basis for scaffolding-mediated assembly and maturation of a dsDNA virus . Proceedings of the National Academy of Sciences of the United States of America vol. 108 , ( 4 ) 1355 - 1360 .

Graham DP, Rezai A, Baker D ( 2011 ) . A hybrid joining scheme for high strength multimaterial joints . Iccm International Conferences on Composite Materials .

Puentes F, van der Star B, Huizinga R, Gerritsen W, van der Valk P ( 2011 ) . Autoimmunity to axonal proteins in multiple sclerosis . MULTIPLE SCLEROSIS JOURNAL vol. 17 , S329 - S329 .

Andreou AP, Supronsinchai W, Lasalandra M ( 2011 ) . Cannabinoid mechanisms of acetaminophen within the trigeminal thalamus . CEPHALALGIA . vol. 31 , 8 - 8 .

Leaver-Fay A, Tyka M, Lewis SM, Lange OF, Thompson J, Jacak R, Kaufman KW, Renfrew PD et al. ( 2011 ) . Chapter nineteen Rosetta3 An Object-Oriented Software Suite for the Simulation and Design of Macromolecules . Computer Methods, Part C , vol. 487 , Elsevier

Baker DJ, Nurok M ( 2011 ) . Chemical and biologic warfare agents: An introduction for anesthesiologists . Essential Clinical Anesthesia ,

Jackson S, Giovannoni G ( 2011 ) . Fingolimod (FTY720) modulates microglial activation to augment markers of remyelination . MULTIPLE SCLEROSIS JOURNAL vol. 17 , S210 - S210 .

Lidster K, Jackson S, Coffey P, Baker M, Garthwaite J, Selwood D, Giovannoni G ( 2011 ) . Neuroprotection in a novel optic neuritis model . MULTIPLE SCLEROSIS JOURNAL vol. 17 , S435 - S435 .

Fishpool DT, Baker D, Ogin SL ( 2011 ) . Preferential energy absorbing interfacesfor ballistic and structural applications . Iccm International Conferences on Composite Materials .

Al-Izki S, Pryce G, Amor S, Gerritsen W, Garthwaite J ( 2011 ) . Selective targeting of neuroprotection to MS lesions: sodium channel blockers in experimental autoimmune encephalomyelitis . MULTIPLE SCLEROSIS JOURNAL vol. 17 , S209 - S210 .

Pryce G, Visintin C, Lutz B, Marsicano G, Selwood DL ( 2011 ) . Selective targeting of spasticity by CNS-excluded cannabinoids . MULTIPLE SCLEROSIS JOURNAL vol. 17 , S247 - S247 .

Baker D, Pryce G, Visintin C, Pertwee RG, Tanner C, Ross R, Irving A, Sisay S ( 2011 ) . VSN16R a novel agent for the control of spasticity . MULTIPLE SCLEROSIS JOURNAL vol. 17 , S243 - S243 .

Kellogg EH, Leaver‐Fay A, Baker D ( 2010 ) . Role of conformational sampling in computing mutation‐induced changes in protein structure and stability . Proteins Structure Function and Bioinformatics vol. 79 , ( 3 ) 830 - 838 .

Weerapana E, Wang C, Simon GM, Richter F, Khare S, Dillon MBD, Bachovchin DA, Mowen K et al. ( 2010 ) . Quantitative reactivity profiling predicts functional cysteines in proteomes . Nature vol. 468 , ( 7325 ) 790 - 795 .

Tyka MD, Keedy DA, André I, DiMaio F, Song Y, Richardson DC, Richardson JS, Baker D ( 2010 ) . Alternate States of Proteins Revealed by Detailed Energy Landscape Mapping . Journal of Molecular Biology vol. 405 , ( 2 ) 607 - 618 .

Liu L, Murphy P, Baker D, Lutz S ( 2010 ) . Computational design of orthogonal nucleoside kinases . Chemical Communications vol. 46 , ( 46 ) 8803 - 8805 .

Ofek G, Guenaga FJ, Schief WR, Skinner J, Baker D, Wyatt R, Kwong PD ( 2010 ) . Elicitation of structure-specific antibodies by epitope scaffolds . Proceedings of the National Academy of Sciences of the United States of America vol. 107 , ( 42 ) 17880 - 17887 .

Baker D ( 2010 ) . An exciting but challenging road ahead for computational enzyme design . Protein Science vol. 19 , ( 10 ) 1817 - 1819 .

Sampathkumar P, Lu F, Zhao X, Li Z, Gilmore J, Bain K, Rutter ME, Gheyi T et al. ( 2010 ) . Structure of a putative BenF‐like porin from Pseudomonas fluorescens Pf‐5 at 2.6 Å resolution . Proteins Structure Function and Bioinformatics vol. 78 , ( 14 ) 3056 - 3062 .

Correia BE, Ban Y-EA, Holmes MA, Xu H, Ellingson K, Kraft Z, Carrico C, Boni E et al. ( 2010 ) . Computational Design of Epitope-Scaffolds Allows Induction of Antibodies Specific for a Poorly Immunogenic HIV Vaccine Epitope . Structure vol. 18 , ( 9 ) 1116 - 1126 .

Baker D, Amor S ( 2010 ) . Editorial: Quality control of experimental autoimmune encephalomyelitis . Multiple Sclerosis vol. 16 , ( 9 ) 1025 - 1027 .

Baker D ( 2010 ) . Quality control of experimental autoimmune encephalomyelitis . Mult Scler vol. 16 , ( 9 ) 1025 - 1027 .

Tang Y, Schneider WM, Shen Y, Raman S, Inouye M, Baker D, Roth MJ, Montelione GT ( 2010 ) . Fully automated high-quality NMR structure determination of small 2H-enriched proteins . Journal of Structural and Functional Genomics vol. 11 , ( 4 ) 223 - 232 .

Kiss G, Röthlisberger D, Baker D, Houk KN ( 2010 ) . Evaluation and ranking of enzyme designs . Protein Science vol. 19 , ( 9 ) 1760 - 1773 .

Fowler DM, Araya CL, Fleishman SJ, Kellogg EH, Stephany JJ, Baker D, Fields S ( 2010 ) . High-resolution mapping of protein sequence-function relationships . Nature Methods vol. 7 , ( 9 ) 741 - 746 .

Sanowar S, Singh P, Pfuetzner RA, André I, Zheng H, Spreter T, Strynadka NCJ, Gonen T et al. ( 2010 ) . Interactions of the Transmembrane Polymeric Rings of the Salmonella enterica Serovar Typhimurium Type III Secretion System . mBio vol. 1 , ( 3 ) 10.1128/mbio.00158 - 10.1128/mbio.00110 .

Cooper S, Khatib F, Treuille A, Barbero J, Lee J, Beenen M, Leaver-Fay A, Baker D et al. ( 2010 ) . Predicting protein structures with a multiplayer online game . Nature vol. 466 , ( 7307 ) 756 - 760 .

Smagghe BJ, Huang P-S, Ban Y-EA, Baker D, Springer TA ( 2010 ) . Modulation of Integrin Activation by an Entropic Spring in the β-Knee* . Journal of Biological Chemistry vol. 285 , ( 43 ) 32954 - 32966 .

Sheffler W, Baker D ( 2010 ) . RosettaHoles2: A volumetric packing measure for protein structure refinement and validation . Protein Science vol. 19 , ( 10 ) 1991 - 1995 .

Siegel JB, Zanghellini A, Lovick HM, Kiss G, Lambert AR, St.Clair JL, Gallaher JL, Hilvert D et al. ( 2010 ) . Computational Design of an Enzyme Catalyst for a Stereoselective Bimolecular Diels-Alder Reaction . Science vol. 329 , ( 5989 ) 309 - 313 .

Cooper S, Treuille A, Barbero J, Leaver-Fay A, Tuite K, Khatib F, Snyder AC, Beenen M et al. ( 2010 ) . The challenge of designing scientific discovery games . Conference: Proceedings of the Fifth International Conference on the Foundations of Digital Games40 - 47 .

Fleishman SJ, Corn JE, Strauch EM, Whitehead TA, Andre I, Thompson J, Havranek JJ, Das R et al. ( 2010 ) . Rosetta in CAPRI rounds 13–19 . Proteins Structure Function and Bioinformatics vol. 78 , ( 15 ) 3212 - 3218 .

Zelter A, Hoopmann MR, Vernon R, Baker D, MacCoss MJ, Davis TN ( 2010 ) . Isotope Signatures Allow Identification of Chemically Cross-Linked Peptides by Mass Spectrometry: A Novel Method to Determine Interresidue Distances in Protein Structures through Cross-Linking . Journal of Proteome Research vol. 9 , ( 7 ) 3583 - 3589 .

Meenan NAG, Sharma A, Fleishman SJ, MacDonald CJ, Morel B, Boetzel R, Moore GR, Baker D et al. ( 2010 ) . The structural and energetic basis for high selectivity in a high-affinity protein-protein interaction . Proceedings of the National Academy of Sciences of the United States of America vol. 107 , ( 22 ) 10080 - 10085 .

Baker DJ, Richards G, Grainger A, Gonzalez P, Brown S, DeFries R, Held A, Ojima D ( 2010 ) . Achieving forest carbon information with higher certainty: A five-part plan . Environmental Science & Policy vol. 13 , ( 3 ) 249 - 260 .

Ashworth J, Taylor GK, Havranek JJ, Quadri SA, Stoddard BL, Baker D ( 2010 ) . Computational reprogramming of homing endonuclease specificity at multiple adjacent base pairs . Nucleic Acids Research vol. 38 , ( 16 ) 5601 - 5608 .

Lassila JK, Baker D, Herschlag D ( 2010 ) . Origins of catalysis by computationally designed retroaldolase enzymes . Proceedings of the National Academy of Sciences of the United States of America vol. 107 , ( 11 ) 4937 - 4942 .

Das R, Karanicolas J, Baker D ( 2010 ) . Atomic accuracy in predicting and designing noncanonical RNA structure . Nature Methods vol. 7 , ( 4 ) 291 - 294 .

Raman S, Lange OF, Rossi P, Tyka M, Wang X, Aramini J, Liu G, Ramelot TA et al. ( 2010 ) . NMR Structure Determination for Larger Proteins Using Backbone-Only Data . Science vol. 327 , ( 5968 ) 1014 - 1018 .

Blum B, Jordan MI, Baker D ( 2010 ) . Feature space resampling for protein conformational search . Proteins Structure Function and Bioinformatics vol. 78 , ( 6 ) 1583 - 1593 .

Amor S, Puentes F, van der Valk P ( 2010 ) . Inflammation in neurodegenerative diseases . IMMUNOLOGY vol. 129 , ( 2 ) 154 - 169 .

Shen Y, Bryan PN, He Y, Orban J, Baker D, Bax A ( 2010 ) . De novo structure generation using chemical shifts for proteins with high‐sequence identity but different folds . Protein Science vol. 19 , ( 2 ) 349 - 356 .

Leung CCY, Kellogg E, Kuhnert A, Hänel F, Baker D, Glover JNM ( 2010 ) . Insights from the crystal structure of the sixth BRCT domain of topoisomerase IIβ binding protein 1 . Protein Science vol. 19 , ( 1 ) 162 - 167 .

Wang C, Vernon R, Lange O, Tyka M, Baker D ( 2010 ) . Prediction of structures of zinc‐binding proteins through explicit modeling of metal coordination geometry . Protein Science vol. 19 , ( 3 ) 494 - 506 .

Khersonsky O, Röthlisberger D, Dym O, Albeck S, Jackson CJ, Baker D, Tawfik DS ( 2009 ) . Evolutionary Optimization of Computationally Designed Enzymes: Kemp Eliminases of the KE07 Series . Journal of Molecular Biology vol. 396 , ( 4 ) 1025 - 1042 .

Raman S, Huang YJ, Mao B, Rossi P, Aramini JM, Liu G, Montelione GT, Baker D ( 2009 ) . Accurate Automated Protein NMR Structure Determination Using Unassigned NOESY Data . Journal of the American Chemical Society vol. 132 , ( 1 ) 202 - 207 .

Das R, André I, Shen Y, Wu Y, Lemak A, Bansal S, Arrowsmith CH, Szyperski T et al. ( 2009 ) . Simultaneous prediction of protein folding and docking at high resolution . Proceedings of the National Academy of Sciences of the United States of America vol. 106 , ( 45 ) 18978 - 18983 .

Krieger E, Joo K, Lee J, Lee J, Raman S, Thompson J, Tyka M, Baker D et al. ( 2009 ) . Improving physical realism, stereochemistry, and side‐chain accuracy in homology modeling: Four approaches that performed well in CASP8 . Proteins Structure Function and Bioinformatics vol. 77 , ( S9 ) 114 - 122 .

Dosenovic P, Guenaga J, Ofek G, Baker D, Schief W, Kwong P, Hedestam GK, Wyatt R ( 2009 ) . P12-12. Analysis of antibody and B cell responses following inoculation with computationally designed HIV-1 2F5 epitope scaffold proteins . Retrovirology vol. 6 , ( Suppl 3 )

Raman S, Vernon R, Thompson J, Tyka M, Sadreyev R, Pei J, Kim D, Kellogg E et al. ( 2009 ) . Structure prediction for CASP8 with all‐atom refinement using Rosetta . Proteins Structure Function and Bioinformatics vol. 77 , ( S9 ) 89 - 99 .

Thyme SB, Jarjour J, Takeuchi R, Havranek JJ, Ashworth J, Scharenberg AM, Stoddard BL, Baker D ( 2009 ) . Exploitation of binding energy for catalysis and design . Nature vol. 461 , ( 7268 ) 1300 - 1304 .

Lapa e Silva JR, Pretolani M, Bachelet CM, Scheper R ( 2009 ) . Booster-Dependent Alterations of the Subsets of T Lymphocytes and Eosinophils in the Bronchi of Immunized Guinea Pigs . International Archives of Allergy and Immunology vol. 99 , ( 2-4 ) 350 - 353 .

Goto K, Kawanabe K, Kowalski R ( 2009 ) . Bonding ability evaluation of bone cement on the cortical surface of rabbit’s tibia . Journal of Materials Science: Materials in Medicine vol. 21 , ( 1 ) 139 - 146 .

Rosato A, Bagaria A, Baker D, Bardiaux B, Cavalli A, Doreleijers JF, Giachetti A, Guerry P et al. ( 2009 ) . CASD-NMR: critical assessment of automated structure determination by NMR . Nature Methods vol. 6 , ( 9 ) 625 - 626 .

Kidd BA, Baker D, Thomas WE ( 2009 ) . Computation of Conformational Coupling in Allosteric Proteins . PLOS Computational Biology vol. 5 , ( 8 )

Davis IW, Raha K, Head MS, Baker D ( 2009 ) . Blind docking of pharmaceutically relevant compounds using RosettaLigand . Protein Science vol. 18 , ( 9 ) 1998 - 2002 .

Kimber I, Foster JR, Turk JL ( 2009 ) . Selective Impairment of T Lymphocyte Activation following Contact Sensitization with Oxazolone . International Archives of Allergy and Applied Immunology vol. 95 , ( 2-3 ) 142 - 148 .

Kimber I, Bentley AN, Ward RK, Baker D, Turk JL ( 2009 ) . Antigen-Restricted Antigenic Competition Induced by 2,4-Dinitrochlorobenzene: Association with Depression of Lymphocyte Proliferation . International Archives of Allergy and Applied Immunology vol. 91 , ( 3 ) 315 - 322 .

Idris AI, Sophocleous A, Landao-Bassonga E, Baker D, van't Hof RJ ( 2009 ) . Cannabinoid Receptor Type 1 Protects against Age-Related Osteoporosis by Regulating Osteoblast and Adipocyte Differentiation in Marrow Stromal Cells . CELL METAB vol. 10 , ( 2 ) 139 - 147 .

Healey DG, Baker D, Gschmeissner SE ( 2009 ) . An Antigenic Determinant Common to Lymphocytes and Langerhans Cells of the Guinea Pig . International Archives of Allergy and Applied Immunology vol. 82 , ( 2 ) 120 - 124 .

Baker D, Healey DG, Verghese S ( 2009 ) . Phenotypic Analysis of Guinea Pig Langerhans Cells with Antibodies Directed against Leucocyte Surface Antigens . International Archives of Allergy and Applied Immunology vol. 86 , ( 3 ) 350 - 355 .

Kim DE, Blum B, Bradley P, Baker D ( 2009 ) . Sampling Bottlenecks in De novo Protein Structure Prediction . Journal of Molecular Biology vol. 393 , ( 1 ) 249 - 260 .

DiMaio F, Tyka MD, Baker ML, Chiu W, Baker D ( 2009 ) . Refinement of Protein Structures into Low-Resolution Density Maps Using Rosetta . Journal of Molecular Biology vol. 392 , ( 1 ) 181 - 190 .

Al-Izki S, Pryce G, Giovannoni G ( 2009 ) . Evaluating potential therapies for bladder dysfunction in a mouse model of multiple sclerosis with high-resolution ultrasonography . Mult Scler vol. 15 , ( 7 ) 795 - 801 .

Murphy PM, Bolduc JM, Gallaher JL, Stoddard BL, Baker D ( 2009 ) . Alteration of enzyme specificity by computational loop remodeling and design . Proceedings of the National Academy of Sciences of the United States of America vol. 106 , ( 23 ) 9215 - 9220 .

Idris AI, Sophocleous A, Landao-Bassonga E, Merkouris M, Baker D, van't Hof RJ ( 2009 ) . Cannabinoid receptor type 1 protects against age-related bone loss by regulating osteoblast and adipocyte differentiation of bone marrow stromal cells . BONE . vol. 44 , S222 - S222 .

Havranek JJ, Baker D ( 2009 ) . Motif‐directed flexible backbone design of functional interactions . Protein Science vol. 18 , ( 6 ) 1293 - 1305 .

Michino M, Abola E, Brooks CL, Dixon JS, Moult J, Stevens RC ( 2009 ) . Community-wide assessment of GPCR structure modelling and ligand docking: GPCR Dock 2008 . Nature Reviews Drug Discovery vol. 8 , ( 6 ) 455 - 463 .

Hooper C, Pinteaux-Jones F, Fry VA, Sevastou IG, BAKER D ( 2009 ) . Differential effects of albumin on microglia and macrophages; implications for neurodegeneration following blood-brain barrier damage . J Neurochem vol. 109 , ( 3 ) 694 - 705 .

Spreter T, Yip CK, Sanowar S, André I, Kimbrough TG, Vuckovic M, Pfuetzner RA, Deng W et al. ( 2009 ) . A conserved structural motif mediates formation of the periplasmic rings in the type III secretion system . Nature Structural & Molecular Biology vol. 16 , ( 5 ) 468 - 476 .

Ashworth J, Baker D ( 2009 ) . Assessment of the optimization of affinity and specificity at protein–DNA interfaces . Nucleic Acids Research vol. 37 , ( 10 ) e73 - e73 .

Nauli S, Kuhlman B, Le Trong I, Stenkamp RE, Teller D, Baker D ( 2009 ) . Crystal structures and increased stabilization of the protein G variants with switched folding pathways NuG1 and NuG2 . Protein Science vol. 11 , ( 12 ) 2924 - 2931 .

Zhu J, Luo B-H, Barth P, Schonbrun J, Baker D, Springer TA ( 2009 ) . The Structure of a Receptor with Two Associating Transmembrane Domains on the Cell Surface: Integrin αIIbβ3 . Molecular Cell vol. 34 , ( 2 ) 234 - 249 .

Muratore KE, Seeliger MA, Wang Z, Fomina D, Neiswinger J, Havranek JJ, Baker D, Kuriyan J et al. ( 2009 ) . Comparative Analysis of Mutant Tyrosine Kinase Chemical Rescue . Biochemistry vol. 48 , ( 15 ) 3378 - 3386 .

Sadreyev RI, Shi S, Baker D, Grishin NV ( 2009 ) . Structure similarity measure with penalty for close non-equivalent residues . Bioinformatics vol. 25 , ( 10 ) 1259 - 1263 .

Dietrich JA, Yoshikuni Y, Fisher KJ, Woolard FX, Ockey D, McPhee DJ, Renninger NS, Chang MCY et al. ( 2009 ) . A Novel Semi-biosynthetic Route for Artemisinin Production Using Engineered Substrate-Promiscuous P450BM3 . ACS Chemical Biology vol. 4 , ( 4 ) 261 - 267 .

Barth P, Wallner B, Baker D ( 2009 ) . Prediction of membrane protein structures with complex topologies using limited constraints . Proceedings of the National Academy of Sciences of the United States of America vol. 106 , ( 5 ) 1409 - 1414 .

Das R, Baker D ( 2009 ) . Prospects for de novo phasing with de novo protein models . Acta Crystallographica Section D, Structural Biology vol. 65 , ( 2 ) 169 - 175 .

Bonneau R, Ruczinski I, Tsai J, Baker D ( 2009 ) . Contact order and ab initio protein structure prediction . Protein Science vol. 11 , ( 8 ) 1937 - 1944 .

Ivankov DN, Garbuzynskiy SO, Alm E, Plaxco KW, Baker D, Finkelstein AV ( 2009 ) . Contact order revisited: Influence of protein size on the folding rate . Protein Science vol. 12 , ( 9 ) 2057 - 2062 .

Amor S ( 2009 ) . Experimental autoimmune encephalomyelitis . Biology of Multiple Sclerosis ,

Wang C, Schueler‐Furman O, Baker D ( 2009 ) . Improved side‐chain modeling for protein–protein docking . Protein Science vol. 14 , ( 5 ) 1328 - 1339 .

Scalley‐Kim M, Minard P, Baker D ( 2009 ) . Low free energy cost of very long loop insertions in proteins . Protein Science vol. 12 , ( 2 ) 197 - 206 .

Zanghellini A, Jiang L, Wollacott AM, Cheng G, Meiler J, Althoff EA, Röthlisberger D, Baker D ( 2009 ) . New algorithms and an in silico benchmark for computational enzyme design . Protein Science vol. 15 , ( 12 ) 2785 - 2794 .

Wollacott AM, Zanghellini A, Murphy P, Baker D ( 2009 ) . Prediction of structures of multidomain proteins from structures of the individual domains . Protein Science vol. 16 , ( 2 ) 165 - 175 .

Sadreyev RI, Baker D, Grishin NV ( 2009 ) . Profile–profile comparisons by COMPASS predict intricate homologies between protein families . Protein Science vol. 12 , ( 10 ) 2262 - 2272 .

Schlosshauer M, Baker D ( 2009 ) . Realistic protein–protein association rates from a simple diffusional model neglecting long‐range interactions, free energy barriers, and landscape ruggedness . Protein Science vol. 13 , ( 6 ) 1660 - 1669 .

Yi Q, Rajagopal P, Klevit RE, Baker D ( 2009 ) . Structural and kinetic characterization of the simplified SH3 domain FP1 . Protein Science vol. 12 , ( 4 ) 776 - 783 .

Warner KJ, Cuschieri J, Garland B, Carlbom D, Baker D, Copass MK, Jurkovich GJ, Bulger EM ( 2009 ) . The Utility of Early End-Tidal Capnography in Monitoring Ventilation Status After Severe Injury . Journal of Trauma and Acute Care Surgery vol. 66 , ( 1 ) 26 - 31 .

Rank JA, Baker D ( 2008 ) . A desolvation barrier to hydrophobic cluster formation may contribute to the rate‐limiting step in protein folding . Protein Science vol. 6 , ( 2 ) 347 - 354 .

Gu H, Yi Q, Bray ST, Shiau AK ( 2008 ) . A phage display system for studying the sequence determinants of protein folding . Protein Science vol. 4 , ( 6 ) 1108 - 1117 .

Minard P, Scalley‐Kim M, Watters A, Baker D ( 2008 ) . A “loop entropy reduction” phage‐display selection for folded amino acid sequences . Protein Science vol. 10 , ( 1 ) 129 - 134 .

Yi Q, Baker D ( 2008 ) . Direct evidence for a two‐state protein unfolding transition from hydrogen‐deuterium exchange, mass spectrometry, and NMR . Protein Science vol. 5 , ( 6 ) 1060 - 1066 .

Gu H, Doshi N, Kim DE, Simons KT, Santiago JV, Nauli S, Baker D ( 2008 ) . Robustness of protein folding kinetics to surface hydrophobic substitutions . Protein Science vol. 8 , ( 12 ) 2734 - 2741 .

Han KE, Bystroff C, Baker D ( 2008 ) . Three‐dimensional structures and contexts associated with recurrent amino acid sequence patterns . Protein Science vol. 6 , ( 7 ) 1587 - 1590 .

Sheffler W, Baker D ( 2008 ) . RosettaHoles: Rapid assessment of protein core packing for structure prediction, refinement, design, and validation . Protein Science vol. 18 , ( 1 ) 229 - 239 .

Andre I, Baker D ( 2008 ) . Computational protein design with rosetta . 5th Conference on Foundations of Nanoscience Self Assembled Architectures and Devices Fnano 2008 . 166 - 167 .

Rigby A, Baker D ( 2008 ) . Targeting EPO to the CNS; development of a novel therapeutic strategy . IMMUNOLOGY . vol. 125 , 134 - 135 .

Mustafa I ( 2008 ) . Ventilator Care in the Developing World . Mechanical Ventilation Clinical Applications and Pathophysiology ,

Shen Y, Vernon R, Baker D, Bax A ( 2008 ) . De novo protein structure generation from incomplete chemical shift assignments . Journal of Biomolecular NMR vol. 43 , ( 2 ) 63 - 78 .

Luo B-H, Karanicolas J, Harmacek LD, Baker D, Springer TA ( 2008 ) . Rationally Designed Integrin β3 Mutants Stabilized in the High Affinity Conformation* . Journal of Biological Chemistry vol. 284 , ( 6 ) 3917 - 3924 .

Davis IW, Baker D ( 2008 ) . RosettaLigand Docking with Full Ligand and Receptor Flexibility . Journal of Molecular Biology vol. 385 , ( 2 ) 381 - 392 .

Baker DJ, Schaefer M, Gibbons JH, Kennedy D ( 2008 ) . Response . Science vol. 322 , ( 5903 ) 855 - 856 .

Alexandrova AN, Röthlisberger D, Baker D, Jorgensen WL ( 2008 ) . Catalytic Mechanism and Performance of Computationally Designed Enzymes for Kemp Elimination . Journal of the American Chemical Society vol. 130 , ( 47 ) 15907 - 15915 .

Ramelot TA, Raman S, Kuzin AP, Xiao R, Ma L, Acton TB, Hunt JF, Montelione GT et al. ( 2008 ) . Improving NMR protein structure quality by Rosetta refinement: A molecular replacement study . Proteins Structure Function and Bioinformatics vol. 75 , ( 1 ) 147 - 167 .

Hampton DW, Anderson J, Pryce G, Giovannoni G, Compston A, Franklin RJM, Baker D ( 2008 ) . An experimental model of secondary progressive multiple sclerosis that shows regional variation in gliosis, remyelination, axonal and neuronal loss . J NEUROIMMUNOL vol. 201 , 200 - 211 .

Sawaya MR, Wojtowicz WM, Andre I, Qian B, Wu W, Baker D, Eisenberg D, Zipursky SL ( 2008 ) . A Double S Shape Provides the Structural Basis for the Extraordinary Binding Specificity of Dscam Isoforms . Cell vol. 134 , ( 6 ) 1007 - 1018 .

Jackson S, Al-Izik S, Pryce G ( 2008 ) . Fingolimod reduces axonal loss in relapsing secondary progressive experimental autoimmune encephalomyelitis . MULTIPLE SCLEROSIS . vol. 14 , S80 - S81 .

Parkes H, Shorter S, So PW, Baker D, Pryce G, Giovannoni G ( 2008 ) . High resolution 1H nuclear magnetic resonance spectroscopic-based metabolomic urine analysis of experimental autoimmune encephalitis, a model disease of multiple sclerosis . MULTIPLE SCLEROSIS . vol. 14 , S86 - S87 .

Baker DJ ( 2008 ) . The Oceanography Society: Its Importance Then and Now . Oceanography vol. 21 , ( 3 ) 22 - 25 .

Al-Izki S, Pryce G, Jackson S ( 2008 ) . Neuroprotective effects of omega-3 fatty acids in a mouse model of multiple sclerosis . JOURNAL OF NEUROIMMUNOLOGY . vol. 197 , 173 - 173 .

Rigby A, Chernajovsky Y, Baker D ( 2008 ) . Targeting EPO to the CNS; Development of a novel therapeutic strategy . JOURNAL OF NEUROIMMUNOLOGY . vol. 197 , 171 - 171 .

Schaefer M, Baker DJ, Gibbons JH, Groat CG, Kennedy D, Kennel CF ( 2008 ) . An Earth Systems Science Agency . Science vol. 321 , ( 5885 ) 44 - 45 .

Anderson JM, Hampton DW, Patani R, Pryce G, Crowther RA, Franklin RJM, Giovannoni G, Baker D et al. ( 2008 ) . Abnormally phosphorylated tau is associated with neuronal and axonal loss in experimental autoimmune encephalomyelitis and multiple sclerosis . BRAIN vol. 131 , 1736 - 1748 .

Pinteaux-Jones F, Sevastou IG, Heales S, Baker D ( 2008 ) . Myelin-induced microglial neurotoxicity can be controlled by microglial metabotropic glutamate receptors . J NEUROCHEM vol. 106 , ( 1 ) 442 - 454 .

BAKER D, O'NEILL JK, TURK JL ( 2008 ) . Control of immune-mediated disease of the central nervous system requires the use of a neuroactive agent: elucidation by the action of mitoxantrone . Clinical & Experimental Immunology vol. 90 , ( 1 ) 124 - 128 .

Betik AC, Baker DJ, Krause DJ ( 2008 ) . Exercise training in late middle‐aged male Fischer 344 × Brown Norway F1‐hybrid rats improves skeletal muscle aerobic function . Quarterly Journal of Experimental Physiology and Cognate Medical Sciences vol. 93 , ( 7 ) 863 - 871 .

Das R, Baker D ( 2008 ) . Macromolecular Modeling with Rosetta . Annual Review of Biochemistry vol. 77 , ( 1 ) 363 - 382 .

Cho HD, Sood VD, Baker D, Weiner AM ( 2008 ) . On the role of a conserved, potentially helix-breaking residue in the tRNA-binding α-helix of archaeal CCA-adding enzymes . RNA vol. 14 , ( 7 ) 1284 - 1289 .

Keeble AH, Joachimiak LA, Maté MJ, Meenan N, Kirkpatrick N, Baker D, Kleanthous C ( 2008 ) . Experimental and Computational Analyses of the Energetic Basis for Dual Recognition of Immunity Proteins by Colicin Endonucleases . Journal of Molecular Biology vol. 379 , ( 4 ) 745 - 759 .

East E, Gverić D, Baker D, Pryce G ( 2008 ) . Chronic relapsing experimental allergic encephalomyelitis (CREAE) in plasminogen activator inhibitor-1 knockout mice: the effect of fibrinolysis during neuroinflammation . Neuropathol Appl Neurobiol vol. 34 , ( 2 ) 216 - 230 .

Shen Y, Lange O, Delaglio F, Rossi P, Aramini JM, Liu G, Eletsky A, Wu Y et al. ( 2008 ) . Consistent blind protein structure generation from NMR chemical shift data . Proceedings of the National Academy of Sciences of the United States of America vol. 105 , ( 12 ) 4685 - 4690 .

Röthlisberger D, Khersonsky O, Wollacott AM, Jiang L, DeChancie J, Betker J, Gallaher JL, Althoff EA et al. ( 2008 ) . Kemp elimination catalysts by computational enzyme design . Nature vol. 453 , ( 7192 ) 190 - 195 .

Das R, Kudaravalli M, Jonikas M, Laederach A, Fong R, Schwans JP, Baker D, Piccirilli JA et al. ( 2008 ) . Structural inference of native and partially folded RNA by high-throughput contact mapping . Proceedings of the National Academy of Sciences of the United States of America vol. 105 , ( 11 ) 4144 - 4149 .

Jiang L, Althoff EA, Clemente FR, Doyle L, Röthlisberger D, Zanghellini A, Gallaher JL, Betker JL et al. ( 2008 ) . De Novo Computational Design of Retro-Aldol Enzymes . Science vol. 319 , ( 5868 ) 1387 - 1391 .

Raman S, Qian B, Baker D, Walker RC ( 2008 ) . Advances in Rosetta protein structure prediction on massively parallel systems . Journal of Research and Development vol. 52 , ( 1.2 ) 7 - 17 .

Croxford JL, Pryce G, Jackson SJ, Ledent C, Giovannoni G ( 2008 ) . Cannabinoid-mediated neuroprotection, not immuno suppression, may be more relevant to multiple sclerosis . J NEUROIMMUNOL vol. 193 , ( 1-2 ) 120 - 129 .

Pryce G, Jackson SJ ( 2008 ) . Cannabinoids for the Control of multiple Sclerosis . Cannabinoids and the Brain , Springer Nature

Blum B, Jordan MI, Kim DE, Das R, Bradley P, Baker D ( 2008 ) . Feature selection methods for improving protein structure prediction with Rosetta . Advances in Neural Information Processing Systems 20 Proceedings of the 2007 Conference .

Fan E, Baker D, Fields S, Gelb MH, Buckner FS, Van Voorhis WC, Phizicky E, Dumont M et al. ( 2008 ) . Structural Genomics of Pathogenic Protozoa: an Overview . Methods in Molecular Biology vol. 426 , 497 - 513 .

Baker D ( 2008 ) . The endocannabinoid system and multiple sclerosis . Curr Pharm Des vol. 14 , ( 23 ) 2326 - 2336 .

Goobes G, Goobes R, Shaw WJ, Gibson JM, Long JR, Raghunathan V, Schueler‐Furman O, Popham JM et al. ( 2008 ) . The structure, dynamics, and energetics of protein adsorption—lessons learned from adsorption of statherin to hydroxyapatite . Magnetic Resonance in Chemistry vol. 45 , ( S1 ) s32 - s47 .

( 2007 ) . Correction for Barth et al., Toward high-resolution prediction and design of transmembrane helical protein structures . Proceedings of the National Academy of Sciences of the United States of America vol. 104 , ( 51 ) 20635 - 20635 .

McBeth C, Seamons A, Pizarro JC, Fleishman SJ, Baker D, Kortemme T, Goverman JM, Strong RK ( 2007 ) . A New Twist in TCR Diversity Revealed by a Forbidden αβ TCR . Journal of Molecular Biology vol. 375 , ( 5 ) 1306 - 1319 .

André I, Bradley P, Wang C, Baker D ( 2007 ) . Prediction of the structure of symmetrical protein assemblies . Proceedings of the National Academy of Sciences of the United States of America vol. 104 , ( 45 ) 17656 - 17661 .

Baker D, Jackson SJ ( 2007 ) . Cannabinoid control of neuroinflammation related to multiple sclerosis . BRIT J PHARMACOL vol. 152 , ( 5 ) 649 - 654 .

Hoi PM, Visintin C, Okuyama M, Gardiner SM, Kaup SS ( 2007 ) . Vascular pharmacology of a novel cannabinoid-like compound, 3-(5-dimethylcarbamoyl-pent-1-enyl)-N-(2-hydroxy-1-methyl-ethyl) benzamide (VSN16) in the rat . BRIT J PHARMACOL vol. 152 , ( 5 ) 751 - 764 .

Wang C, Schueler‐Furman O, Andre I, London N, Fleishman SJ, Bradley P, Qian B, Baker D ( 2007 ) . RosettaDock in CAPRI rounds 6–12 . Proteins Structure Function and Bioinformatics . vol. 69 , 758 - 763 .

Qian B, Raman S, Das R, Bradley P, McCoy AJ, Read RJ, Baker D ( 2007 ) . High-resolution structure prediction and the crystallographic phase problem . Nature vol. 450 , ( 7167 ) 259 - 264 .

Knight JDR, Qian B, Baker D, Kothary R ( 2007 ) . Conservation, Variability and the Modeling of Active Protein Kinases . PLOS ONE vol. 2 , ( 10 )

Barth P, Schonbrun J, Baker D ( 2007 ) . Toward high-resolution prediction and design of transmembrane helical protein structures . Proceedings of the National Academy of Sciences of the United States of America vol. 104 , ( 40 ) 15682 - 15687 .

Das R, Qian B, Raman S, Vernon R, Thompson J, Bradley P, Khare S, Tyka MD et al. ( 2007 ) . Structure prediction for CASP7 targets using extensive all‐atom refinement with Rosetta@home . Proteins Structure Function and Bioinformatics . vol. 69 , 118 - 128 .

Das R, Baker D ( 2007 ) . Automated de novo prediction of native-like RNA tertiary structures . Proceedings of the National Academy of Sciences of the United States of America vol. 104 , ( 37 ) 14664 - 14669 .

Wojtowicz WM, Wu W, Andre I, Qian B, Baker D, Zipursky SL ( 2007 ) . A Vast Repertoire of Dscam Binding Specificities Arises from Modular Interactions of Variable Ig Domains . Cell vol. 130 , ( 6 ) 1134 - 1145 .

Lengyel CSE, Willis LJ, Mann P, Baker D, Kortemme T, Strong RK, McFarland BJ ( 2007 ) . Mutations Designed to Destabilize the Receptor-Bound Conformation Increase MICA-NKG2D Association Rate and Affinity* . Journal of Biological Chemistry vol. 282 , ( 42 ) 30658 - 30666 .

Tress M, Cheng J, Baldi P, Joo K, Lee J, Seo J, Lee J, Baker D et al. ( 2007 ) . Assessment of predictions submitted for the CASP7 domain prediction category . Proteins Structure Function and Bioinformatics . vol. 69 , 137 - 151 .

Wang C, Bradley P, Baker D ( 2007 ) . Protein–Protein Docking with Backbone Flexibility . Journal of Molecular Biology vol. 373 , ( 2 ) 503 - 519 .

Pocock JM, Pinteaux-Jones F, Fry VA ( 2007 ) . Metabotropic glutamate receptors on microglia: Switching off toxicity . JOURNAL OF NEUROCHEMISTRY . vol. 102 , 239 - 239 .

Stankunas K, Bayle JH, Havranek JJ, Wandless TJ, Baker D, Crabtree GR, Gestwicki JE ( 2007 ) . Rescue of Degradation‐Prone Mutants of the FK506‐Rapamycin Binding (FRB) Protein with Chemical Ligands . ChemBioChem vol. 8 , ( 10 ) 1162 - 1169 .

Li J, Shinjo M, Matsumura Y, Morita M, Baker D, Ikeguchi M, Kihara H ( 2007 ) . An α-Helical Burst in the src SH3 Folding Pathway . Biochemistry vol. 46 , ( 17 ) 5072 - 5082 .

Baker DJ ( 2007 ) . The Management of Casualties Following Toxic Agent Release: The Approach Adopted in France . Chemical Warfare Agents , Wiley

Maresz K, Pryce G, Ponomarev ED, Marsicano G, Croxford JL, Shriver LP, Cheng XD, Carrier EJ et al. ( 2007 ) . Direct suppression of CNS autoimmune inflammation via the cannabinoid receptor CB1 on neurons and CB2 on autoreactive T cells . NAT MED vol. 13 , ( 4 ) 492 - 497 .

Malmström L, Riffle M, Strauss CEM, Chivian D, Davis TN, Bonneau R, Baker D ( 2007 ) . Superfamily Assignments for the Yeast Proteome through Integration of Structure Prediction with the Gene Ontology . PLOS Biology vol. 5 , ( 4 )

Yatsenko AS, Gray EE, Shcherbata HR, Patterson LB, Sood VD, Kucherenko MM, Baker D, Ruohola-Baker H ( 2007 ) . A Putative Src Homology 3 Domain Binding Motif but Not the C-terminal Dystrophin WW Domain Binding Motif Is Required for Dystroglycan Function in Cellular Polarity in Drosophila * . Journal of Biological Chemistry vol. 282 , ( 20 ) 15159 - 15169 .

Pryce G ( 2007 ) . Control of spasticity in a multiple sclerosis model is mediated by CB1, not CB2, cannabinoid receptors . BRIT J PHARMACOL vol. 150 , ( 4 ) 519 - 525 .

Watters AL, Deka P, Corrent C, Callender D, Varani G, Sosnick T, Baker D ( 2007 ) . The Highly Cooperative Folding of Small Naturally Occurring Proteins Is Likely the Result of Natural Selection . vol. 128 , is. 3 , pp. 613 - 624 . Elsevier

Shcherbata HR, Yatsenko AS, Patterson L, Sood VD, Nudel U, Yaffe D, Baker D, Ruohola‐Baker H ( 2007 ) . Dissecting muscle and neuronal disorders in a Drosophila model of muscular dystrophy . The EMBO Journal vol. 26 , ( 2 ) 481 - 493 .

Alverson K ( 2006 ) . Taking the Pulse of the Oceans . Science vol. 314 , ( 5806 ) 1657 - 1657 .

Dantas G, Corrent C, Reichow SL, Havranek JJ, Eletr ZM, Isern NG, Kuhlman B, Varani G et al. ( 2006 ) . High-resolution Structural and Thermodynamic Analysis of Extreme Stabilization of Human Procarboxypeptidase by Computational Protein Design . Journal of Molecular Biology vol. 366 , ( 4 ) 1209 - 1221 .

Goobes G, Goobes R, Schueler-Furman O, Baker D, Stayton PS, Drobny GP ( 2006 ) . Folding of the C-terminal bacterial binding domain in statherin upon adsorption onto hydroxyapatite crystals . Proceedings of the National Academy of Sciences of the United States of America vol. 103 , ( 44 ) 16083 - 16088 .

Baker ML, Jiang W, Wedemeyer WJ, Rixon FJ, Baker D, Chiu W ( 2006 ) . Ab Initio Modeling of the Herpesvirus VP26 Core Domain Assessed by CryoEM Density . PLOS Computational Biology vol. 2 , ( 10 )

Bradley P, Baker D ( 2006 ) . Improved beta‐protein structure prediction by multilevel optimization of nonlocal strand pairings and local backbone conformation . Proteins Structure Function and Bioinformatics vol. 65 , ( 4 ) 922 - 929 .

Baker DJ ( 2006 ) . Elevated caspase and AIF gene expression correlate with progression of sarcopenia during aging in male F344BN rats . Experimental Gerontology vol. 41 , ( 11 ) 1149 - 1156 .

Meiler J, Baker D ( 2006 ) . ROSETTALIGAND: Protein–small molecule docking with full side‐chain flexibility . Proteins Structure Function and Bioinformatics vol. 65 , ( 3 ) 538 - 548 .

Baker D, Croxford JL, Pryce G, Jackson SM, Ledent C, Lutz B, Pertwee RG ( 2006 ) . Cannabinoid-mediated immunosuppression in experimental allergic encephalomyelitis . JOURNAL OF NEUROIMMUNOLOGY . vol. 178 , 90 - 91 .

Baker D ( 2006 ) . Protection of axonal damage in experimental antoimmune encephalomyelitis . MULTIPLE SCLEROSIS . vol. 12 , S12 - S13 .

Baker D ( 2006 ) . Role of immunity in neurodegeneration in autoimmune encephalomyelitis . JOURNAL OF NEUROIMMUNOLOGY . vol. 178 , 20 - 20 .

Cabranes A, Pryce G, Baker D, Fernandez-Ruiz J ( 2006 ) . Changes in CB1 receptors in motor-related brain structures of chronic relapsing experimental allergic encephalomyelitis mice . BRAIN RES vol. 1107 , 199 - 205 .

Chivian D, Baker D ( 2006 ) . Homology modeling using parametric alignment ensemble generation with consensus and energy-based model selection . Nucleic Acids Research vol. 34 , ( 17 ) e112 - e112 .

Dantas G, Watters AL, Lunde BM, Eletr ZM, Isern NG, Roseman T, Lipfert J, Doniach S et al. ( 2006 ) . Mis-translation of a Computationally Designed Protein Yields an Exceptionally Stable Homodimer: Implications for Protein Engineering and Evolution . Journal of Molecular Biology vol. 362 , ( 5 ) 1004 - 1024 .

Baker DJ, Krause DJ ( 2006 ) . No Decline in Skeletal Muscle Oxidative Capacity With Aging in Long-Term Calorically Restricted Rats: Effects Are Independent of Mitochondrial DNA Integrity . The Journals of Gerontology Series A vol. 61 , ( 7 ) 675 - 684 .

Baker D ( 2006 ) . Proteins by design . Scientist vol. 20 , ( 7 ) 26 - 32 .

Hepple RT, Baker DJ, McConkey M, Murynka T ( 2006 ) . Caloric Restriction Protects Mitochondrial Function with Aging in Skeletal and Cardiac Muscles . Rejuvenation Research . vol. 9 , 219 - 222 .

Ashworth J, Havranek JJ, Duarte CM, Sussman D, Monnat RJ, Stoddard BL, Baker D ( 2006 ) . Computational redesign of endonuclease DNA binding and cleavage specificity . Nature vol. 441 , ( 7093 ) 656 - 659 .

Bio FAB Group, Baker D, Church G, Collins J, Endy D, Jacobson J ( 2006 ) . Engineering Life: Building a FAB for Biology . Scientific American vol. 294 , ( 6 ) 44 - 51 .

Joachimiak LA, Kortemme T, Stoddard BL, Baker D ( 2006 ) . Computational Design of a New Hydrogen Bond Network and at Least a 300-fold Specificity Switch at a Protein−Protein Interface . Journal of Molecular Biology vol. 361 , ( 1 ) 195 - 208 .

Yarov-Yarovoy V, Baker D, Catterall WA ( 2006 ) . Voltage sensor conformations in the open and closed states in rosetta structural models of K+ channels . Proceedings of the National Academy of Sciences of the United States of America vol. 103 , ( 19 ) 7292 - 7297 .

Sprague ER, Wang C, Baker D, Bjorkman PJ ( 2006 ) . Crystal Structure of the HSV-1 Fc Receptor Bound to Fc Reveals a Mechanism for Antibody Bipolar Bridging . PLOS Biology vol. 4 , ( 6 )

Palmer AE, Giacomello M, Kortemme T, Hires SA, Lev-Ram V, Baker D, Tsien RY ( 2006 ) . Ca2+ Indicators Based on Computationally Redesigned Calmodulin-Peptide Pairs . Cell Chemical Biology vol. 13 , ( 5 ) 521 - 530 .

Dobson N, Dantas G, Baker D, Varani G ( 2006 ) . High-Resolution Structural Validation of the Computational Redesign of Human U1A Protein . Structure vol. 14 , ( 5 ) 847 - 856 .

Bilsland LG, Dick JRT, Pryce G, Petrosino S, Di Marzo V ( 2006 ) . Increasing cannabinoid levels by pharmacological and genetic manipulation delay disease progression in SOD1 mice . FASEB J vol. 20 , ( 7 ) 1003 - + .

Misura KMS, Chivian D, Rohl CA, Kim DE, Baker D ( 2006 ) . Physically realistic homology models built with rosetta can be more accurate than their templates . Proceedings of the National Academy of Sciences of the United States of America vol. 103 , ( 14 ) 5361 - 5366 .

Baker DJ, Greenhaff PL, Timmons JA ( 2006 ) . Glycogen phosphorylase inhibition as a therapeutic target: a review of the recent patent literature . Expert Opinion on Therapeutic Patents vol. 16 , ( 4 ) 459 - 466 .

Baker DJ, Krause DJ, Howlett RA ( 2006 ) . Nitric oxide synthase inhibition reduces O2 cost of force development and spares high‐energy phosphates following contractions in pump‐perfused rat hindlimb muscles . Quarterly Journal of Experimental Physiology and Cognate Medical Sciences vol. 91 , ( 3 ) 581 - 589 .

Thompson MJ, Sievers SA, Karanicolas J, Ivanova MI, Baker D, Eisenberg D ( 2006 ) . The 3D profile method for identifying fibril-forming segments of proteins . Proceedings of the National Academy of Sciences of the United States of America vol. 103 , ( 11 ) 4074 - 4078 .

Arakaki T, Le Trong I, Phizicky E, Quartley E, DeTitta G, Luft J, Lauricella A, Anderson L et al. ( 2006 ) . Structure of Lmaj006129AAA, a hypothetical protein from Leishmania major . Acta Crystallographica Section F: Structural Biology Communications vol. 62 , ( 3 ) 175 - 179 .

Morozov AV, Tsemekhman K, Baker D ( 2006 ) . Electron Density Redistribution Accounts for Half the Cooperativity of α Helix Formation . The Journal of Physical Chemistry B vol. 110 , ( 10 ) 4503 - 4505 .

Baker D ( 2006 ) . Prediction and design of macromolecular structures and interactions . Philosophical Transactions of the Royal Society B Biological Sciences vol. 361 , ( 1467 ) 459 - 463 .

Sood VD, Baker D ( 2006 ) . Recapitulation and Design of Protein Binding Peptide Structures and Sequences . Journal of Molecular Biology vol. 357 , ( 3 ) 917 - 927 .

Baker D, Pryce G, Yamamura T ( 2006 ) . Cannabinoid-mediated immunosuppression in experimental allergic encephalomyelitits . CURRENT TOPICS IN NEUROIMMUNOLOGY . 109 - 116 .

Cristino L, De Petrocellis L, Pryce G, Baker D, Guglielmotti V ( 2006 ) . Immunohistochemical localization of cannabinoid type 1 and vanilloid transient receptor potential vanilloid type 1 receptors in the mouse brain . NEUROSCIENCE vol. 139 , ( 4 ) 1405 - 1415 .

Baker D, Pryce G, Davies WL ( 2006 ) . In silico patent searching reveals a new cannabinoid receptor . TRENDS PHARMACOL SCI vol. 27 , ( 1 ) 1 - 4 .

Ligresti A, Cascio MG, Kulasegram S, Beletskaya I, De Petrocellis L, Saha B, Mahadevan A, Visintin C et al. ( 2006 ) . New potent and selective inhibitors of anandamide reuptake with antispastic activity in a mouse model of multiple sclerosis . BRIT J PHARMACOL vol. 147 , ( 1 ) 83 - 91 .

Li W, Wang T, Li E, Baker D, Jin L, Ge S, Chen Y, Zhang Y ( 2006 ) . Parallelization and Performance Characterization of Protein 3D Structure Prediction of Rosetta . Conference: Proceedings 20th IEEE International Parallel & Distributed Processing Symposium1 - 8 .

Walker RC, Raman S ( 2006 ) . Poster reception---High resolution, high throughput protein structure prediction using IBM Blue Gene supercomputers . Conference: Proceedings of the 2006 ACM/IEEE conference on Supercomputing - SC '06165 - es .

de Lago E, Fernandez-Ruiz J, Ortega-Gutierrez S, Cabranes A, Pryce G, Baker D ( 2006 ) . UCM707, an inhibitor of the anandamide uptake, behaves as a symptom control agent in models of Huntington's disease and multiple sclerosis, but fails to delay/arrest the progression of different motor-related disorders . EUR NEUROPSYCHOPHARM vol. 16 , ( 1 ) 7 - 18 .

Yarov‐Yarovoy V, Schonbrun J, Baker D ( 2005 ) . Multipass membrane protein structure prediction using Rosetta . Proteins Structure Function and Bioinformatics vol. 62 , ( 4 ) 1010 - 1025 .

Song G, Lazar GA, Kortemme T, Shimaoka M, Desjarlais JR, Baker D, Springer TA ( 2005 ) . Rational Design of Intercellular Adhesion Molecule-1 (ICAM-1) Variants for Antagonizing Integrin Lymphocyte Function-associated Antigen-1-dependent Adhesion* . Journal of Biological Chemistry vol. 281 , ( 8 ) 5042 - 5049 .

Preece NE, Amor S, Baker D, Gadian DG, O'Neill JK ( 2005 ) . Experimental encephalomyelitis modulates inositol and taurine in the spinal cord of biozzi mice . Magnetic Resonance in Medicine vol. 32 , ( 6 ) 692 - 697 .

Baker D, Taylor WR ( 2005 ) . Ab initio structure prediction . Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics , Wiley

Schueler-Furman O, Wang C, Bradley P, Misura K, Baker D ( 2005 ) . Progress in Modeling of Protein Structures and Interactions . Science vol. 310 , ( 5748 ) 638 - 642 .

Lacy DB, Lin HC, Melnyk RA, Schueler-Furman O, Reither L, Cunningham K, Baker D, Collier RJ ( 2005 ) . A model of anthrax toxin lethal factor bound to protective antigen . Proceedings of the National Academy of Sciences of the United States of America vol. 102 , ( 45 ) 16409 - 16414 .

Morozov AV, Havranek JJ, Baker D, Siggia ED ( 2005 ) . Protein–DNA binding specificity predictions with structural models . Nucleic Acids Research vol. 33 , ( 18 ) 5781 - 5798 .

Cheng G, Qian B, Samudrala R, Baker D ( 2005 ) . Improvement in protein functional site prediction by distinguishing structural and functional constraints on protein family evolution using computational design . Nucleic Acids Research vol. 33 , ( 18 ) 5861 - 5867 .

Heijmans N, Smith PA, Morris-Downes MM, Pryce G, Donaldson AVJ ( 2005 ) . Encephalitogenic and tolerogenic potential of altered peptide ligands of MOG and PLP in Biozzi ABH mice . J NEUROIMMUNOL vol. 167 , ( 1-2 ) 23 - 33 .

Baker DJ ( 2005 ) . The Versatility of the Pump-Perfused Rat Hindlimb Preparation: Examples Relating to Skeletal Muscle Function and Energy Metabolism . Applied Physiology Nutrition and Metabolism . vol. 30 , 576 - 590 .

Bradley P, Misura KMS, Baker D ( 2005 ) . Toward High-Resolution de Novo Structure Prediction for Small Proteins . Science vol. 309 , ( 5742 ) 1868 - 1871 .

Carli P, Baker DJ ( 2005 ) . Managing mass casualties following toxic agent release . International Journal of Intensive Care vol. 12 , ( 3 )

East E, Baker D, Pryce G, Lijnen HR, Gverić D ( 2005 ) . A role for the plasminogen activator system in inflammation and neurodegeneration in the central nervous system during experimental allergic encephalomyelitis . Am J Pathol vol. 167 , ( 2 ) 545 - 554 .

Pryce G, O'Neill JK, Croxford JL, Amor S, East E ( 2005 ) . Autoimmune tolerance eliminates relapses but fails to halt progression in a model of multiple sclerosis . J NEUROIMMUNOL vol. 165 , ( 1-2 ) 41 - 52 .

Amor S, Smith PA, 't Hart B ( 2005 ) . Biozzi mice: Of mice and human neurological diseases . J NEUROIMMUNOL vol. 165 , ( 1-2 ) 1 - 10 .

Baker DJ ( 2005 ) . The French prehospital emergency medicine system (SAMU): An introduction . CPD Anaesthesia vol. 7 , ( 1 ) 20 - 25 .

Smith PA, Morris-Downes M, Heijmans N, Pryce G, Arter E, O'Neill JK, Baker D ( 2005 ) . Epitope spread is not critical for the relapse and progression of MOG 8-21 induced EAE in Biozzi ABH mice . J NEUROIMMUNOL vol. 164 , ( 1-2 ) 76 - 84 .

Idris AI, Hof RJV, Greig IR, Ridge SA, Baker D ( 2005 ) . Regulation of bone mass, bone loss and osteoclast activity by cannabinoid receptors . NAT MED vol. 11 , ( 7 ) 774 - 779 .

Schueler‐Furman O, Wang C, Baker D ( 2005 ) . Progress in protein–protein docking: Atomic resolution predictions in the CAPRI experiment using RosettaDock with an improved treatment of side‐chain flexibility . Proteins Structure Function and Bioinformatics . vol. 60 , 187 - 194 .

Jackson SJ, Diemel LT, Pryce G ( 2005 ) . Cannabinoids and neuroprotection in CNS inflammatory disease . JOURNAL OF THE NEUROLOGICAL SCIENCES . vol. 233 , 21 - 25 .

Hepple RT, Baker DJ, Kaczor JJ, Krause DJ ( 2005 ) . Long‐term caloric restriction abrogates the age‐related decline in skeletal muscle aerobic function . The FASEB Journal vol. 19 , ( 10 ) 1320 - 1322 .

Idris AI, Van't Hof RJ, Greig IR, Ridge SA, Ross RA ( 2005 ) . Cannabinoid receptor 1 knockout mice have increased bone mass and are protected from ovariectomy-induced bone loss . BONE . vol. 36 , S132 - S132 .

Korkegian A, Black ME, Baker D, Stoddard BL ( 2005 ) . Computational Thermostabilization of an Enzyme . Science vol. 308 , ( 5723 ) 857 - 860 .

Pryce G ( 2005 ) . Emerging properties of cannabinoid medicines in management of multiple sclerosis . TRENDS NEUROSCI vol. 28 , ( 5 ) 272 - 276 .

Visintin C, Aliev AE, Riddall D, Baker D, Hoi PM ( 2005 ) . Membrane receptor probes: Solid-phase synthesis of biotin-Asp-PEG-arvanil derivatives . ORG LETT vol. 7 , ( 9 ) 1699 - 1702 .

Meiler J, Baker D ( 2005 ) . The fumarate sensor DcuS: progress in rapid protein fold elucidation by combining protein structure prediction methods with NMR spectroscopy . Journal of Magnetic Resonance . vol. 173 , 310 - 316 .

Baker D ( 2005 ) . The problem of secondary contamination following chemical agent release . Critical Care vol. 9 , ( 4 )

Gegg ME, Harry R, Hankey D, Zambarakji H, Pryce G, Baker D ( 2005 ) . Suppression of autoimmune retinal disease by lovastatin does not require Th2 cytokine induction . J IMMUNOL vol. 174 , ( 4 ) 2327 - 2335 .

Misura KMS, Baker D ( 2005 ) . Progress and challenges in high‐resolution refinement of protein structure models . Proteins Structure Function and Bioinformatics vol. 59 , ( 1 ) 15 - 29 .

Chivian D, Robertson T, Bonneau R, Baker D ( 2005 ) . Ab Initio Methods . Structural Bioinformatics ,

Jiang L, Kuhlman B, Kortemme T, Baker D ( 2005 ) . A “solvated rotamer” approach to modeling water‐mediated hydrogen bonds at protein–protein interfaces . Proteins Structure Function and Bioinformatics vol. 58 , ( 4 ) 893 - 904 .

Saunders CT, Baker D ( 2005 ) . Recapitulation of Protein Family Divergence using Flexible Backbone Protein Design . Journal of Molecular Biology vol. 346 , ( 2 ) 631 - 644 .

Kim DE, Chivian D, Malmström L, Baker D ( 2005 ) . Automated prediction of domain boundaries in CASP6 targets using Ginzu and RosettaDOM . Proteins Structure Function and Bioinformatics . vol. 61 , 193 - 200 .

Graña O, Baker D, MacCallum RM, Meiler J, Punta M, Rost B, Tress ML, Valencia A ( 2005 ) . CASP6 assessment of contact prediction . Proteins Structure Function and Bioinformatics . vol. 61 , 214 - 224 .

Jackson SJ, Pryce G, Baker D ( 2005 ) . Cannabinoid-receptor 1 null mice are susceptible to neurofilament damage and caspase 3 activation . NEUROSCIENCE vol. 134 , ( 1 ) 261 - 268 .

Constantinescu CS, Baker D ( 2005 ) . Cytokines in Experimental Autoimmune Encephalomyelitis . Experimental Models of Multiple Sclerosis , Springer Nature

Liu CZ, Green SM, Watkins ND, Baker D ( 2005 ) . Dynamic creep and mechanical characteristics of SmartSet GHV bone cement . Journal of Materials Science: Materials in Medicine vol. 16 , ( 2 ) 153 - 160 .

Bradley P, Malmström L, Qian B, Schonbrun J, Chivian D, Kim DE, Meiler J, Misura KMS et al. ( 2005 ) . Free modeling with Rosetta in CASP6 . Proteins Structure Function and Bioinformatics . vol. 61 , 128 - 134 .

Baker D ( 2005 ) . Genetics of Experimental Allergic Encephalomyelitis . Experimental Models of Multiple Sclerosis , Springer Nature

Chivian D, Kim DE, Malmström L, Schonbrun J, Rohl CA, Baker D ( 2005 ) . Prediction of CASP6 structures using automated robetta protocols . Proteins Structure Function and Bioinformatics . vol. 61 , 157 - 166 .

Cazzanti L, Gupta M, Malmström L, Baker D ( 2005 ) . Quality Assessment of Low Free-Energy Protein Structure Predictions . Conference: 2005 IEEE Workshop on Machine Learning for Signal Processing375 - 380 .

Havranek JJ, Duarte CM, Baker D ( 2004 ) . A Simple Physical Model for the Prediction and Design of Protein–DNA Interactions . Journal of Molecular Biology vol. 344 , ( 1 ) 59 - 70 .

Jackson SJ, Baker D ( 2004 ) . Cannabinoid-mediated neuroprotection following interferon-gamma treatment in a three-dimensional mouse brain aggregate cell culture . EUR J NEUROSCI vol. 20 , ( 9 ) 2267 - 2275 .

Hagen JL, Krause DJ, Baker DJ, Tarnopolsky MA ( 2004 ) . Skeletal Muscle Aging in F344BN F1-Hybrid Rats: I. Mitochondrial Dysfunction Contributes to the Age-Associated Reduction in VO2max . The Journals of Gerontology Series A vol. 59 , ( 11 ) 1099 - 1110 .

Hepple RT, Hagen JL, Krause DJ ( 2004 ) . Skeletal Muscle Aging in F344BN F1-Hybrid Rats: II. Improved Contractile Economy in Senescence Helps Compensate for Reduced ATP-Generating Capacity . The Journals of Gerontology Series A vol. 59 , ( 11 ) 1111 - 1119 .

Qian B, Ortiz AR, Baker D ( 2004 ) . Improvement of comparative model accuracy by free-energy optimization along principal components of natural structural variation . Proceedings of the National Academy of Sciences of the United States of America vol. 101 , ( 43 ) 15346 - 15351 .

Idris AI, Van't Hof' RJ, Greig IR, Ross RA ( 2004 ) . Regulation of osteoclastic bone resorption and bone mass by the cannabinoid receptor 1 pathway . JOURNAL OF BONE AND MINERAL RESEARCH . vol. 19 , S284 - S284 .

Chen Y, Kortemme T, Robertson T, Baker D, Varani G ( 2004 ) . A new hydrogen-bonding potential for the design of protein–RNA interactions predicts specific contacts and discriminates decoys . Nucleic Acids Research vol. 32 , ( 17 ) 5147 - 5162 .

Misura KMS, Morozov AV, Baker D ( 2004 ) . Analysis of Anisotropic Side-chain Packing in Proteins and Application to High-resolution Structure Prediction . Journal of Molecular Biology vol. 342 , ( 2 ) 651 - 664 .

Pryce G, Jackson SM, Giovannoni G ( 2004 ) . Cannabinoids are neuroprotective: dissociation of true neuroprotection from protection secondary to immunosuppression . JOURNAL OF NEUROIMMUNOLOGY . vol. 154 , 78 - 78 .

Heijmans N, Smith P, Pryce D, Baker D, Morris-Downes M ( 2004 ) . Non-encephalitogenic single amino acid substitutions of MOG 8-21 and PLP 56-70 suppress relapsing EAE in ABH mice . JOURNAL OF NEUROIMMUNOLOGY . vol. 154 , 60 - 60 .

Baker D, Pryce G ( 2004 ) . The potential role of the endocannabinoid system in the control of multiple scleorsis . Current Medicinal Chemistry Central Nervous System Agents vol. 4 , ( 3 ) 195 - 202 .

East E, Baker D, Pryce G ( 2004 ) . The role of plasminogen activators in experimental allergic encephalomyelitis: inflammation and axonal pathology . JOURNAL OF NEUROIMMUNOLOGY . vol. 154 , 167 - 167 .

Roques A, Browne M, Taylor A ( 2004 ) . Quantitative measurement of the stresses induced during polymerisation of bone cement . Biomaterials vol. 25 , ( 18 ) 4415 - 4424 .

Ellmerich S, Takacs K, Mycko M, Waldner H, Wahid F, Boyton RJ, Smith PA, Baker D et al. ( 2004 ) . Disease-related epitope spread in a humanized T cell receptor transgenic model of multiple sclerosis . EUR J IMMUNOL vol. 34 , ( 7 ) 1839 - 1848 .

Kim DE, Chivian D, Baker D ( 2004 ) . Protein structure prediction and analysis using the Robetta server . Nucleic Acids Research vol. 32 , ( suppl_2 ) w526 - w531 .

von Grotthuss M, Wyrwicz LS, Pas J, Rychlewski L ( 2004 ) . Predicting Protein Structures Accurately . Science vol. 304 , ( 5677 ) 1597 - 1599 .

Morozov AV, Misura KMS, Tsemekhman K, Baker D ( 2004 ) . Comparison of Quantum Mechanics and Molecular Mechanics Dimerization Energy Landscapes for Pairs of Ring-Containing Amino Acids in Proteins . The Journal of Physical Chemistry B vol. 108 , ( 24 ) 8489 - 8496 .

Watters AL, Baker D ( 2004 ) . Searching for folded proteins in vitro and in silico . vol. 271 , is. 9 , pp. 1615 - 1622 . Wiley

Morozov AV, Kortemme T, Tsemekhman K, Baker D ( 2004 ) . Close agreement between the orientation dependence of hydrogen bonds observed in protein structures and quantum mechanical calculations . Proceedings of the National Academy of Sciences of the United States of America vol. 101 , ( 18 ) 6946 - 6951 .

Scalley-Kim M, Baker D ( 2004 ) . Characterization of the Folding Energy Landscapes of Computer Generated Proteins Suggests High Folding Free Energy Barriers and Cooperativity may be Consequences of Natural Selection . Journal of Molecular Biology vol. 338 , ( 3 ) 573 - 583 .

Rohl CA, Strauss CEM, Chivian D, Baker D ( 2004 ) . Modeling structurally variable regions in homologous proteins with rosetta . Proteins Structure Function and Bioinformatics vol. 55 , ( 3 ) 656 - 677 .

Kortemme T, Joachimiak LA, Bullock AN, Schuler AD, Stoddard BL, Baker D ( 2004 ) . Computational redesign of protein-protein interaction specificity . Nature Structural & Molecular Biology vol. 11 , ( 4 ) 371 - 379 .

Svensson HG, Wedemeyer WJ, Ekstrom JL, Callender DR, Kortemme T, Kim DE, Sjöbring U, Baker D ( 2004 ) . Contributions of Amino Acid Side Chains to the Kinetics and Thermodynamics of the Bivalent Binding of Protein L to Ig κ Light Chain † . Biochemistry vol. 43 , ( 9 ) 2445 - 2457 .

Ginalski K, Rychlewski L, Baker D, Grishin NV ( 2004 ) . Protein structure prediction for the male-specific region of the human Y chromosome . Proceedings of the National Academy of Sciences of the United States of America vol. 101 , ( 8 ) 2305 - 2310 .

Kortemme T, Kim DE, Baker D ( 2004 ) . Computational Alanine Scanning of Protein-Protein Interfaces . Science Signaling vol. 2004 , ( 219 )

Baker D, Silen JL, Agard DA ( 2004 ) . Protease pro region required for folding is a potent inhibitor of the mature enzyme . Proteins Structure Function and Bioinformatics vol. 12 , ( 4 ) 339 - 344 .

Kortemme T, Baker D ( 2004 ) . Computational design of protein–protein interactions . Current Opinion in Chemical Biology vol. 8 , ( 1 ) 91 - 97 .

Kuhlman B, Baker D ( 2004 ) . Exploring folding free energy landscapes using computational protein design . Current Opinion in Structural Biology vol. 14 , ( 1 ) 89 - 95 .

Baker D, Eaton WA ( 2004 ) . Folding and binding . Current Opinion in Structural Biology vol. 14 , ( 1 ) 67 - 69 .

de Lago E, Ligresti A, Ortar G, Morera E, Bifulco M, Di Marzo V ( 2004 ) . In vivo pharmacological actions of two novel inhibitors of anandamide cellular uptake . EUR J PHARMACOL vol. 484 , ( 2-3 ) 249 - 257 .

Rohl CA, Strauss CEM, Misura KMS, Baker D ( 2004 ) . Protein Structure Prediction Using Rosetta . Methods in Enzymology vol. 383 , 66 - 93 .

Kuhn M, Meiler J, Baker D ( 2003 ) . Strand‐loop‐strand motifs: Prediction of hairpins and diverging turns in proteins . Proteins Structure Function and Bioinformatics vol. 54 , ( 2 ) 282 - 288 .

Meiler J, Baker D ( 2003 ) . Rapid protein fold determination using unassigned NMR data . Proceedings of the National Academy of Sciences of the United States of America vol. 100 , ( 26 ) 15404 - 15409 .

Hazbun TR, Malmström L, Anderson S, Graczyk BJ, Fox B, Riffle M, Sundin BA, Aranda JD et al. ( 2003 ) . Assigning Function to Yeast Proteins by Integration of Technologies . Molecular Cell vol. 12 , ( 6 ) 1353 - 1365 .

Wilkinson JD, Whalley BJ, Baker D, Pryce G, Constanti A ( 2003 ) . Medicinal cannabis: is Delta(9)-tetrahydrocannabinol necessary for all its effects? . J PHARM PHARMACOL vol. 55 , ( 12 ) 1687 - 1694 .

Kuhlman B, Dantas G, Ireton GC, Varani G, Stoddard BL, Baker D ( 2003 ) . Design of a Novel Globular Protein Fold with Atomic-Level Accuracy . Science vol. 302 , ( 5649 ) 1364 - 1368 .

Chivian D, Kim DE, Malmström L, Bradley P, Robertson T, Murphy P, Strauss CEM, Bonneau R et al. ( 2003 ) . Automated prediction of CASP‐5 structures using the Robetta server . Proteins Structure Function and Bioinformatics . vol. 53 , 524 - 533 .

Bradley P, Chivian D, Meiler J, Misura KMS, Rohl CA, Schief WR, Wedemeyer WJ, Schueler‐Furman O et al. ( 2003 ) . Rosetta predictions in CASP5: Successes, failures, and prospects for complete automation . Proteins Structure Function and Bioinformatics . vol. 53 , 457 - 468 .

Meiler J, Baker D ( 2003 ) . Coupled prediction of protein secondary and tertiary structure . Proceedings of the National Academy of Sciences of the United States of America vol. 100 , ( 21 ) 12105 - 12110 .

Pryce G, Ahmed Z, Hankey DJR, Jackson SJ, Croxford JL, Ledent C, Thompson AJ, Giovannoni G ( 2003 ) . Cannabinoids inhibit neurodegeneration in models of multiple sclerosis . BRAIN vol. 126 , 2191 - 2202 .

Wedemeyer WJ, Baker D ( 2003 ) . Efficient minimization of angle‐dependent potentials for polypeptides in internal coordinates . Proteins Structure Function and Bioinformatics vol. 53 , ( 2 ) 262 - 272 .

Dantas G, Kuhlman B, Callender D, Wong M, Baker D ( 2003 ) . A Large Scale Test of Computational Protein Design: Folding and Stability of Nine Completely Redesigned Globular Proteins . Journal of Molecular Biology vol. 332 , ( 2 ) 449 - 460 .

Boulanger MJ, Bankovich AJ, Kortemme T, Baker D, Garcia KC ( 2003 ) . Convergent Mechanisms for Recognition of Divergent Cytokines by the Shared Signaling Receptor gp130 . Molecular Cell vol. 12 , ( 3 ) 577 - 589 .

Craner MJ, Kataoka Y, Lo AC, Black JA, Waxman SG ( 2003 ) . Temporal course of upregulation of Na-v 1.8 in Purkinje neurons parallels the progression of clinical deficit in experimental allergic encephalomyelitis . J NEUROPATH EXP NEUR vol. 62 , ( 9 ) 968 - 975 .

East E, Baker D, Pryce GM, Cuzner ML ( 2003 ) . The role of plasminogen activators in experimental allergic encephalomyelitis . GLIA . 40 - 40 .

Tsai J, Bonneau R, Morozov AV, Kuhlman B, Rohl CA, Baker D ( 2003 ) . An improved protein decoy set for testing energy functions for protein structure prediction . Proteins Structure Function and Bioinformatics vol. 53 , ( 1 ) 76 - 87 .

Gray JJ, Moughon S, Wang C, Schueler-Furman O, Kuhlman B, Rohl CA, Baker D ( 2003 ) . Protein–Protein Docking with Simultaneous Optimization of Rigid-body Displacement and Side-chain Conformations . Journal of Molecular Biology vol. 331 , ( 1 ) 281 - 299 .

Ahmed Z, Baker D ( 2003 ) . Interleukin-12 induces mild experimental allergic encephalomyelitis following local central nervous system injury in the Lewis rat . J NEUROIMMUNOL vol. 140 , ( 1-2 ) 109 - 117 .

Kinch LN, Baker D, Grishin NV ( 2003 ) . Deciphering a novel thioredoxin‐like fold family . Proteins Structure Function and Bioinformatics vol. 52 , ( 3 ) 323 - 331 .

Schueler‐Furman O, Baker D ( 2003 ) . Conserved residue clustering and protein structure prediction . Proteins Structure Function and Bioinformatics vol. 52 , ( 2 ) 225 - 235 .

Giovannoni G ( 2003 ) . Inflammatory disorders of the central nervous system . CURR OPIN NEUROL vol. 16 , ( 3 ) 347 - 350 .

Millet O, Mittermaier A, Baker D, Kay LE ( 2003 ) . The Effects of Mutations on Motions of Side-chains in Protein L Studied by 2H NMR Dynamics and Scalar Couplings . Journal of Molecular Biology vol. 329 , ( 3 ) 551 - 563 .

Gray JJ, Moughon SE, Kortemme T, Schueler‐Furman O, Misura KMS, Morozov AV, Baker D ( 2003 ) . Protein–protein docking predictions for the CAPRI experiment . Proteins Structure Function and Bioinformatics vol. 52 , ( 1 ) 118 - 122 .

Hall RJ, Hollis-Moffatt JE, Green RA, Baker D ( 2003 ) . An autoimmune diabetes locus (Idd21) on mouse Chromosome 18 . MAMM GENOME vol. 14 , ( 5 ) 335 - 339 .

Baker D ( 2003 ) . Gene therapy in autoimmune, demyelinating disease of the central nervous system . GENE THER vol. 10 , ( 10 ) 844 - 853 .

Greenwood J, Walters CE, Pryce G, Kanuga N, Beraud E, Baker D ( 2003 ) . Lovastatin inhibits brain endothelial cell Rho-mediated lymphocyte migration and attenuates experimental autoimmune encephalomyelitis . FASEB J vol. 17 , ( 8 ) 905 - 907 .

Pryce G, Baker D ( 2003 ) . Mifepristone or inhibition of 11 beta-hydroxylase activity potentiates the sedating effects of the cannabinoid receptor-1 agonist Delta(9)-tetrahydrocannabinol in mice . NEUROSCI LETT vol. 341 , ( 2 ) 164 - 166 .

Petzold A, Baker D, Pryce G, Thompson EJ ( 2003 ) . Quantification of neurodegeneration by measurement of brain-specific proteins . J NEUROIMMUNOL vol. 138 , ( 1-2 ) 45 - 48 .

Baker D, Pryce G, Giovannoni G ( 2003 ) . The therapeutic potential of cannabis . LANCET NEUROL vol. 2 , ( 5 ) 291 - 298 .

McFarland BJ, Kortemme T, Yu SF, Baker D, Strong RK ( 2003 ) . Symmetry Recognizing Asymmetry Analysis of the Interactions between the C-Type Lectin-like Immunoreceptor NKG2D and MHC Class I-like Ligands . Structure vol. 11 , ( 4 ) 411 - 422 .

Baker D, Pryce G ( 2003 ) . The therapeutic potential of cannabis in multiple sclerosis . EXPERT OPIN INV DRUG vol. 12 , ( 4 ) 561 - 567 .

Craner MJ, Lo AC, Black JA, Cuzner ML ( 2003 ) . Annexin II/piII is up-regulated in Purkinje cells in EAE and MS . NEUROREPORT vol. 14 , ( 4 ) 555 - 558 .

Morozov AV, Kortemme T, Baker D ( 2003 ) . Evaluation of Models of Electrostatic Interactions in Proteins . The Journal of Physical Chemistry B vol. 107 , ( 9 ) 2075 - 2090 .

Kortemme T, Morozov AV, Baker D ( 2003 ) . An Orientation-dependent Hydrogen Bonding Potential Improves Prediction of Specificity and Structure for Proteins and Protein–Protein Complexes . Journal of Molecular Biology vol. 326 , ( 4 ) 1239 - 1259 .

Baker D, Adamson P ( 2003 ) . Potential of statins for the treatment of multiple sclerosis . LANCET NEUROL vol. 2 , ( 1 ) 9 - 10 .

Shirley P ( 2003 ) . Treatment of biological and chemical casualties in the UK . British Journal of Anaesthesia vol. 90 , ( 1 ) 106 - 107 .

Ahmed Z, Doward AI, Pryce G, Pocock JM ( 2002 ) . A role for caspase-1 and-3 in the pathology of experimental allergic encephalomyelitis - Inflammation versus degeneration . AM J PATHOL vol. 161 , ( 5 ) 1577 - 1586 .

Schlosshauer M, Baker D ( 2002 ) . A General Expression for Bimolecular Association Rates with Orientational Constraints . The Journal of Physical Chemistry B vol. 106 , ( 46 ) 12079 - 12083 .

Kortemme T, Baker D ( 2002 ) . A simple physical model for binding energy hot spots in protein–protein complexes . Proceedings of the National Academy of Sciences of the United States of America vol. 99 , ( 22 ) 14116 - 14121 .

Hall RJ, Hollis-Moffat JE, Merriman ME, Bridges RJ, Baker D ( 2002 ) . An autoimmune diabetes locus (ldd21) on mouse chromosome 18 . AMERICAN JOURNAL OF HUMAN GENETICS . vol. 71 , 446 - 446 .

Chevalier BS, Kortemme T, Chadsey MS, Baker D, Monnat RJ, Stoddard BL ( 2002 ) . Design, Activity, and Structure of a Highly Specific Artificial Endonuclease . Molecular Cell vol. 10 , ( 4 ) 895 - 905 .

Bonneau R, Strauss CEM, Rohl CA, Chivian D, Bradley P, Malmström L, Robertson T, Baker D ( 2002 ) . De Novo Prediction of Three-dimensional Structures for Major Protein Families . Journal of Molecular Biology vol. 322 , ( 1 ) 65 - 78 .

Saunders CT, Baker D ( 2002 ) . Evaluation of Structural and Evolutionary Contributions to Deleterious Mutation Prediction . Journal of Molecular Biology vol. 322 , ( 4 ) 891 - 901 .

Alm E, Morozov AV, Kortemme T, Baker D ( 2002 ) . Simple Physical Models Connect Theory and Experiment in Protein Folding Kinetics . Journal of Molecular Biology vol. 322 , ( 2 ) 463 - 476 .

Baker DJ ( 2002 ) . Editorial I Management of casualties from terrorist chemical and biological attack: a key role for the anaesthetist . British Journal of Anaesthesia vol. 89 , ( 2 ) 211 - 214 .

Schonbrun J, Wedemeyer WJ, Baker D ( 2002 ) . Protein structure prediction in 2002 . Current Opinion in Structural Biology vol. 12 , ( 3 ) 348 - 354 .

Kuhlman B, O'Neill JW, Kim DE, Zhang KYJ, Baker D ( 2002 ) . Erratum: Conversion of monomeric protein L to an obligate dimer by computational protein design (Proceedings of the National Academy of Sciences of the United States of America (September 11, 2001) 98:19 (10687-10691)) . Proceedings of the National Academy of Sciences of the United States of America vol. 99 , ( 11 )

Thompson AJ, Baker D ( 2002 ) . Cannabinoids in MS - Potentially useful but not just yet! . NEUROLOGY vol. 58 , ( 9 ) 1323 - 1324 .

Ruczinski I, Kooperberg C, Bonneau R, Baker D ( 2002 ) . Distributions of beta sheets in proteins with application to structure prediction . Proteins Structure Function and Bioinformatics vol. 48 , ( 1 ) 85 - 97 .

Baker D, Agard DA ( 2002 ) . Kinetics versus thermodynamics in protein folding . Biochemistry vol. 33 , ( 24 ) 7505 - 7509 .

Krantz BA, Srivastava AK, Nauli S, Baker D, Sauer RT, Sosnick TR ( 2002 ) . Understanding protein hydrogen bond formation with kinetic H/D amide isotope effects . Nature Structural & Molecular Biology vol. 9 , ( 6 ) 458 - 463 .

Walters CE, Pryce G, Hankey DJR, Sebti SM, Hamilton AD ( 2002 ) . Inhibition of Rho GTPases with protein prenyltransferase inhibitors prevents leukocyte recruitment to the central nervous system and attenuates clinical signs of disease in an animal model of multiple sclerosis . J IMMUNOL vol. 168 , ( 8 ) 4087 - 4094 .

Morris-Downes MM, Smith PA, Rundle JL, Piddlesden SJ, Pham-Dinh D ( 2002 ) . Pathological and regulatory effects of anti-myelin antibodies in experimental allergic encephalomyelitis in mice . J NEUROIMMUNOL vol. 125 , ( 1-2 ) 114 - 124 .

Youssef F, Seifalian AM, Jagroop IA, Hamilton G ( 2002 ) . The early effect of lipid-lowering treatment on carotid and femoral intima media thickness (IMT)dagger . EUR J VASC ENDOVASC vol. 23 , ( 4 ) 358 - 364 .

Brooks JW, Pryce G, Bisogno T, Jaggar SI, Hankey DJR, Bridges D, Ledent C, Bifulco M ( 2002 ) . Arvanil-induced inhibition of spasticity and persistent pain: evidence for therapeutic sites of action different from the vanilloid VR1 receptor and cannabinoid CB1/CB2 receptors . EUR J PHARMACOL vol. 439 , ( 1-3 ) 83 - 92 .

Rohl CA, Baker D ( 2002 ) . De Novo Determination of Protein Backbone Structure from Residual Dipolar Couplings Using Rosetta . Journal of the American Chemical Society vol. 124 , ( 11 ) 2723 - 2729 .

Baker D, Lim WA ( 2002 ) . From folding towards function . Current Opinion in Structural Biology vol. 12 , ( 1 ) 11 - 13 .

Larson SM, Ruczinski I, Davidson AR, Baker D, Plaxco KW ( 2002 ) . Residues participating in the protein folding nucleus do not exhibit preferential evolutionary conservation 1 1 Edited by C. R. Matthews . Journal of Molecular Biology vol. 316 , ( 2 ) 225 - 233 .

Kuhlman B, O’Neill JW, Kim DE, Zhang KYJ, Baker D ( 2002 ) . Accurate computer-based design of a new backbone conformation in the second turn of protein L11Edited by F. Cohen . Journal of Molecular Biology vol. 315 , ( 3 ) 471 - 477 .

Morris-Downes MM, McCormack K, Baker D ( 2002 ) . Encephalitogenic and immunogenic potential of myelin-associated glycoprotein (MAG), oligodendrocyte-specific glycoprotein (OSP) and 2 ',3 '-cyclic nucleotide 3 '-phosphodiesterase (CNPase) in ABH and SJL mice . J NEUROIMMUNOL vol. 122 , ( 1-2 ) 20 - 33 .

Bonneau R, Tsai J, Ruczinski I, Chivian D, Rohl C, Strauss CEM, Baker D ( 2002 ) . Rosetta in CASP4: Progress in ab initio protein structure prediction . Proteins Structure Function and Bioinformatics vol. 45 , ( S5 ) 119 - 126 .

Gårdelöf B, Baker DJ ( 2001 ) . Mechanical ventilation during transport of critically ill patients . International Journal of Intensive Care vol. 8 , ( 3 ) 178 - 179 .

O'Neill JW, Kim DE, Johnsen K ( 2001 ) . Single-Site Mutations Induce 3D Domain Swapping in the B1 Domain of Protein L from Peptostreptococcus magnus . Structure vol. 9 , ( 11 ) 1017 - 1027 .

Baker D, Sali A ( 2001 ) . Protein Structure Prediction and Structural Genomics . Science vol. 294 , ( 5540 ) 93 - 96 .

Lee MR, Tsai J, Baker D, Kollman PA ( 2001 ) . Molecular dynamics in the endgame of protein structure prediction11Edited by B. Honig . Journal of Molecular Biology vol. 313 , ( 2 ) 417 - 430 .

Hankey DJR, Nickerson JM, Donoso LA, Lightman SL ( 2001 ) . Experimental autoimmune uveoretinitis in mice (Biozzi ABH and NOD) expressing the autoimmune-associated H-2A(g7) molecule: identification of a uveitogenic epitope . J NEUROIMMUNOL vol. 118 , ( 2 ) 212 - 222 .

Kuhlman B, O'Neill JW, Kim DE, Zhang KYJ, Baker D ( 2001 ) . Conversion of monomeric protein L to an obligate dimer by computational protein design . Proceedings of the National Academy of Sciences of the United States of America vol. 98 , ( 19 ) 10687 - 10691 .

Nauli S, Kuhlman B, Baker D ( 2001 ) . Computer-based redesign of a protein folding pathway . Nature Structural & Molecular Biology vol. 8 , ( 7 ) 602 - 605 .

Bonneau R, Baker D ( 2001 ) . AB INITIO PROTEIN STRUCTURE PREDICTION: Progress and Prospects . Annual Review of Biophysics vol. 30 , ( 1 ) 173 - 189 .

Ahmed Z, Gveric D, Pryce G, Baker D, Leonard JP ( 2001 ) . Myelin/axonal pathology in interleukin-12 induced serial relapses of experimental allergic encephalomyelitis in the Lewis rat . Am J Pathol vol. 158 , ( 6 ) 2127 - 2138 .

Bonneau R, Tsai J, Ruczinski I, Baker D ( 2001 ) . Functional Inferences from Blind ab Initio Protein Structure Predictions . Journal of Structural Biology vol. 134 , ( 2-3 ) 186 - 190 .

Kim KM, Yi EC, Baker D, Zhang KYJ ( 2001 ) . Post-translational modification of the N-terminal His tag interferes with the crystallization of the wild-type and mutant SH3 domains from chicken src tyrosine kinase . Acta Crystallographica Section D, Structural Biology vol. 57 , ( 5 ) 759 - 762 .

O'Neill JW, Kim DE, Baker D, Zhang KYJ ( 2001 ) . Structures of the B1 domain of protein L from Peptostreptococcus magnus with a tyrosine to tryptophan substitution . Acta Crystallographica Section D, Structural Biology vol. 57 , ( 4 ) 480 - 487 .

Croxford JL, Chernajovsky Y, Baker D ( 2001 ) . Different therapeutic outcomes in experimental allergic encephalomyelitis dependant upon the mode of delivery of IL-10: A comparison of the effects of protein, adenoviral or retroviral IL-10 delivery into the central nervous system . J IMMUNOL vol. 166 , ( 6 ) 4124 - 4130 .

Reichel MB, Bainbridge J, Baker D, Ali RR ( 2001 ) . An immune response after intraocular administration of an adenoviral vector containing a beta galactosidase reporter gene slows retinal degeneration in the rd mouse . BRIT J OPHTHALMOL vol. 85 , ( 3 ) 341 - 344 .

Hankey DJR, Lightman SL ( 2001 ) . Interphotoreceptor retinoid binding protein peptide-induced uveitis in B10.RIII mice: Characterization of disease parameters and immunomodulation . EXP EYE RES vol. 72 , ( 3 ) 341 - 350 .

Simons KT, Strauss C, Baker D ( 2001 ) . Prospects for ab initio protein structural genomics1 1Edited by B. Honig . Journal of Molecular Biology vol. 306 , ( 5 ) 1191 - 1199 .

Grantcharova VP, Baker D ( 2001 ) . Circularization changes the folding transition state of the src SH3 domain11Edited by C. R. Matthews . Journal of Molecular Biology vol. 306 , ( 3 ) 555 - 563 .

Baker D, Pryce G, Brown P, Pertwee RG, Makriyannis A, Khanolkar A, Layward L, Fezza F ( 2001 ) . Endocannabinoids control spasticity in a multiple sclerosis model . FASEB J vol. 15 , ( 2 ) 300 - 302 .

Grantcharova V, Alm EJ, Baker D, Horwich AL ( 2001 ) . Mechanisms of protein folding . Current Opinion in Structural Biology vol. 11 , ( 1 ) 70 - 82 .

Fischer D, Baker D, Moult J ( 2001 ) . We need both computer models and experiments . Nature vol. 409 , ( 6820 ) 558 - 558 .

Lee MR, Baker D, Kollman PA ( 2001 ) . 2.1 and 1.8 Å Average Cα RMSD Structure Predictions on Two Small Proteins, HP-36 and S15 . Journal of the American Chemical Society vol. 123 , ( 6 ) 1040 - 1046 .

Baker DJ ( 2001 ) . Emergency management of injury from the release of toxic substances: Medical aspects of the HAZMAT system . Prehospital Trauma Care ,

Generini S, Matucci-Cerinic M, Partsch G, Stancikova M, Konttinen YT, Rovensky J, Baker DJ ( 2001 ) . Evidence for hyaluronan production in the air pouch model in rats . Clinical and Experimental Rheumatology vol. 19 , ( 3 ) 271 - 276 .

Bonneau R, Strauss CEM, Baker D ( 2001 ) . Improving the performance of rosetta using multiple sequence alignment information and global measures of hydrophobic core formation . Proteins Structure Function and Bioinformatics vol. 43 , ( 1 ) 1 - 11 .

Bowers PM, Strauss CEM, Baker D ( 2000 ) . De novo protein structure determination using sparse NMR data . Journal of Biomolecular NMR vol. 18 , ( 4 ) 311 - 318 .

Baker DJ ( 2000 ) . Emergency ventilation . vol. 7 , is. 4 , pp. 229 - 232 .

Kuhlman B, Baker D ( 2000 ) . Erratum: Native protein sequences are close to optimal for their structures (Proceedings of the National Academy of Sciences of the United States of America (September 12, 2000) 97 (10383-10388)) . Proceedings of the National Academy of Sciences of the United States of America vol. 97 , ( 24 )

Black JA, Baker D, Newcombe J, Cuzner ML ( 2000 ) . Sensory neuron-specific sodium channel SNS is abnormally expressed in the brains of mice with experimental allergic encephalomyelitis and humans with multiple sclerosis . Proceedings of the National Academy of Sciences of the United States of America vol. 97 , ( 21 ) 11598 - 11602 .

Kuhlman B, Baker D ( 2000 ) . Native protein sequences are close to optimal for their structures . Proceedings of the National Academy of Sciences of the United States of America vol. 97 , ( 19 ) 10383 - 10388 .

Plaxco KW, Simons KT, Ruczinski I, Baker D ( 2000 ) . Topology, Stability, Sequence, and Length: Defining the Determinants of Two-State Protein Folding Kinetics . Biochemistry vol. 39 , ( 37 ) 11177 - 11183 .

McCallister EL, Alm E, Baker D ( 2000 ) . Critical role of β-hairpin formation in protein G folding . Nature Structural & Molecular Biology vol. 7 , ( 8 ) 669 - 673 .

Bystroff C, Thorsson V, Baker D ( 2000 ) . HMMSTR: a hidden Markov model for local sequence-structure correlations in proteins11Edited by J. Thornton . Journal of Molecular Biology vol. 301 , ( 1 ) 173 - 190 .

Grantcharova VP, Riddle DS, Baker D ( 2000 ) . Long-range order in the src SH3 folding transition state . Proceedings of the National Academy of Sciences of the United States of America vol. 97 , ( 13 ) 7084 - 7089 .

Chernajovsky Y, Dreja H, Daly G, Annenkov A, Gould D, Adams G, Croxford JL, Baker D et al. ( 2000 ) . Immuno- and genetic therapy in autoimmune diseases . Genes Immun vol. 1 , ( 5 ) 295 - 307 .

Yi Q, Scalley-Kim ML, Alm EJ, Baker D ( 2000 ) . NMR characterization of residual structure in the denatured state of protein L11Edited by P. E. Wright . Journal of Molecular Biology vol. 299 , ( 5 ) 1341 - 1351 .

Baker D ( 2000 ) . Reply: a sanguine approach to cannabis . Trends Pharmacol Sci vol. 21 , ( 6 )

Kim DE, Fisher C, Baker D ( 2000 ) . A breakdown of symmetry in the folding transition state of protein L11Edited by C. R. Matthews . Journal of Molecular Biology vol. 298 , ( 5 ) 971 - 984 .

Baker D ( 2000 ) . A surprising simplicity to protein folding . Nature vol. 405 , ( 6782 ) 39 - 42 .

Johnsen K, O'Neill JW, Kim DE, Baker D, Zhang KYJ ( 2000 ) . Crystallization and preliminary X-ray diffraction studies of mutants of B1 IgG-binding domain of protein L from Peptostreptococcus magnus . Acta Crystallographica Section D, Structural Biology vol. 56 , ( 4 ) 506 - 508 .

Plaxco KW, Larson S, Ruczinski I, Riddle DS, Thayer EC, Buchwitz B, Davidson AR, Baker D ( 2000 ) . Evolutionary conservation in protein folding kinetics11Edited by C. R. Matthews . Journal of Molecular Biology vol. 298 , ( 2 ) 303 - 312 .

Baker D, Pryce G, Croxford JL, Brown P, Pertwee RG, Layward L ( 2000 ) . Cannabinoids control spasticity and tremor in a multiple sclerosis model . Nature vol. 404 , ( 6773 ) 84 - 87 .

Croxford JL, Triantaphyllopoulos KA, Neve RM, Chernajovsky Y ( 2000 ) . Gene therapy for chronic relapsing experimental allergic encephalomyelitis using cells expressing a novel soluble p75 dimeric TNF receptor . J Immunol vol. 164 , ( 5 ) 2776 - 2781 .

Thayer EC, Bystroff C, Baker D ( 2000 ) . Detection of Protein Coding Sequences Using a Mixture Model for Local Protein Amino Acid Sequence . Journal of Computational Biology vol. 7 , ( 1-2 ) 317 - 327 .

Thoua NM, van Noort JM, Baker D, Bose A, van Sechel AC, van Stipdonk MJB, Travers PJ ( 2000 ) . Encephalitogenic and immunogenic potential of the stress protein αB-crystallin in Biozzi ABH (H-2A<SUP>g7</SUP>) mice . JOURNAL OF NEUROIMMUNOLOGY vol. 104 , ( 1 ) 47 - 57 .

Tillan D, Baker DJ ( 2000 ) . Mechanical ventilation during transport of critically ill patients . International Journal of Intensive Care vol. 7 , ( 1 ) 59 - 64 .

Chernajovsky Y, Gould D, Annenkov A, Dreja H, Daly G, Rabinovich GA, Croxford L, Baker D et al. ( 1999 ) . Immunotherapy of auto-immune diseases by gene transfer . Biochem Soc Trans vol. 27 , ( 6 ) 869 - 873 .

Carli P ( 1999 ) . Trauma . vol. 5 , is. 6 , Wolters Kluwer

Brennan FR, O'Neill JK, Allen SJ, Nuki G ( 1999 ) . CD44 is involved in selective leucocyte extravasation during inflammatory central nervous system disease . Immunology vol. 98 , ( 3 ) 427 - 435 .

Scalley ML, Nauli S, Gladwin ST, Baker D ( 1999 ) . Structural Transitions in the Protein L Denatured State Ensemble . Biochemistry vol. 38 , ( 48 ) 15927 - 15935 .

Simons KT, Bonneau R, Ruczinski I, Baker D ( 1999 ) . Ab initio protein structure prediction of CASP III targets using ROSETTA . Proteins Structure Function and Bioinformatics vol. 37 , ( S3 ) 171 - 176 .

Riddle DS, Grantcharova VP, Santiago JV, Alm E, Ruczinski I, Baker D ( 1999 ) . Experiment and theory highlight role of native state topology in SH3 folding . Nature Structural & Molecular Biology vol. 6 , ( 11 ) 1016 - 1024 .

Baker DJ ( 1999 ) . Editorial . Resuscitation vol. 42 , ( 2 ) 101 - 102 .

Chernajovsky Y, Gould D, Annenkov A, Dreja H, Daly G, Rabinovich GA, Croxford L, Baker D et al. ( 1999 ) . IMMUNOTHERAPY OF AUTOIMMUNE DISEASES BY GENE TRANSFER . Biochemical Society Transactions vol. 27 , ( 5 ) a137 - a137 .

Simons KT, Ruczinski I, Kooperberg C, Fox BA, Bystroff C, Baker D ( 1999 ) . Improved recognition of native‐like protein structures using a combination of sequence‐dependent and sequence‐independent features of proteins . Proteins Structure Function and Bioinformatics vol. 34 , ( 1 ) 82 - 95 .

Baker DJ ( 1999 ) . Management of respiratory failure in toxic disasters . Resuscitation . vol. 42 , 125 - 131 .

Baker DJ ( 1999 ) . The pre-hospital management of injury following mass toxic release; a comparison of military and civil approaches . Resuscitation . vol. 42 , 155 - 159 .

Alm E, Baker D ( 1999 ) . Prediction of protein-folding mechanisms from free-energy landscapes derived from native structures . Proceedings of the National Academy of Sciences of the United States of America vol. 96 , ( 20 ) 11305 - 11310 .

Tsai J, Levitt M, Baker D ( 1999 ) . Hierarchy of structure loss in MD simulations of src SH3 domain unfolding11Edited by B. Honig . Journal of Molecular Biology vol. 291 , ( 1 ) 215 - 225 .

Baker D, DeGrado WF ( 1999 ) . Engineering and design . Current Opinion in Structural Biology vol. 9 , ( 4 ) 485 - 486 .

Plaxco KW, Millett IS, Segel DJ, Doniach S, Baker D ( 1999 ) . Chain collapse can occur concomitantly with the rate-limiting step in protein folding . Nature Structural & Molecular Biology vol. 6 , ( 6 ) 554 - 556 .

Alm E, Baker D ( 1999 ) . Matching theory and experiment in protein folding . Current Opinion in Structural Biology vol. 9 , ( 2 ) 189 - 196 .

Bystroff C, Baker D ( 1998 ) . Blind predictions of local protein structure in CASP2 targets using the I‐sites library . Proteins Structure Function and Bioinformatics vol. 29 , ( S1 ) 167 - 171 .

Doyle R, Simons K, Qian H, Baker D ( 1998 ) . Local interactions and the optimization of protein folding . Proteins Structure Function and Bioinformatics vol. 29 , ( 3 ) 282 - 291 .

Croxford JL, O'Neill JK, Browne K, Byrnes AP, Dallman MJ, Wood MJ ( 1998 ) . Local gene therapy with CTLA4-immunoglobulin fusion protein in experimental allergic encephalomyelitis . Eur J Immunol vol. 28 , ( 12 ) 3904 - 3916 .

Baker D ( 1998 ) . Metastable states and folding free energy barriers . Nature Structural & Molecular Biology vol. 5 , ( 12 ) 1021 - 1024 .

Kim DE, Yi Q, Gladwin ST, Goldberg JM, Baker D ( 1998 ) . The single helix in protein L is largely disrupted at the rate-limiting step in folding 1 1 Edited by P. E. Wright . Journal of Molecular Biology vol. 284 , ( 3 ) 807 - 815 .

Plaxco KW, Baker D ( 1998 ) . Limited internal friction in the rate-limiting step of a two-state protein folding reaction . Proceedings of the National Academy of Sciences of the United States of America vol. 95 , ( 23 ) 13591 - 13596 .

Yi Q, Bystroff C, Rajagopal P, Klevit RE, Baker D ( 1998 ) . Prediction and structural characterization of an independently folding substructure in the src SH3 domain11Edited by P. E. Wright . Journal of Molecular Biology vol. 283 , ( 1 ) 293 - 300 .

Shortle D, Simons KT, Baker D ( 1998 ) . Clustering of low-energy conformations near the native structures of small proteins . Proceedings of the National Academy of Sciences of the United States of America vol. 95 , ( 19 ) 11158 - 11162 .

Croxford JL, Ali R, Byrnes A, Baker D ( 1998 ) . Adenoviral gene therapy of experimental allergic encephalomyelitis (EAE) with CTLA4-Ig . Journal of Neuroimmunology vol. 90 , ( 1 )

Thoua N-M, van Noort J, van Sechel A, van Stipdonk M ( 1998 ) . Encephalitogenicity of the stress protein α-Crystallin in biozzi ABH mice . Journal of Neuroimmunology vol. 90 , ( 1 )

Croxford JL, Triantaphyllopolous K, Chernajovsky Y ( 1998 ) . Gene therapy of experimental allergic encephalomyelitis (EAE) with dimeric TNF receptors using cells as biological pumps . Journal of Neuroimmunology vol. 90 , ( 1 )

Grantcharova VP, Riddle DS, Santiago JV, Baker D ( 1998 ) . Important role of hydrogen bonds in the structurally polarized transition state for folding of the src SH3 domain . Nature Structural & Molecular Biology vol. 5 , ( 8 ) 714 - 720 .

Bystroff C, Baker D ( 1998 ) . Prediction of local structure in proteins using a library of sequence-structure motifs11Edited by J. Thornton . Journal of Molecular Biology vol. 281 , ( 3 ) 565 - 577 .

Cazalaà JB ( 1998 ) . Design flaw in continuous syringe pumps . Intensive Care Medicine vol. 24 , ( 6 ) 646 - 647 .

Croxford JL, Triantaphyllopoulos K, Podhajcer OL, Feldmann M ( 1998 ) . Cytokine gene therapy in experimental allergic encephalomyelitis by injection of plasmid DNA-cationic liposome complex into the central nervous system . J Immunol vol. 160 , ( 10 ) 5181 - 5187 .

Kim DE, Gu H, Baker D ( 1998 ) . The sequences of small proteins are not extensively optimized for rapid folding by natural selection . Proceedings of the National Academy of Sciences of the United States of America vol. 95 , ( 9 ) 4982 - 4986 .

Plaxco KW, Simons KT, Baker D ( 1998 ) . Contact order, transition state placement and the refolding rates of single domain proteins11Edited by P. E. Wright . Journal of Molecular Biology vol. 277 , ( 4 ) 985 - 994 .

Rank JA, Baker D ( 1998 ) . Contributions of solvent–solvent hydrogen bonding and van der Waals interactions to the attraction between methane molecules in water . Biophysical Chemistry vol. 71 , ( 2-3 ) 199 - 204 .

Baker D ( 1998 ) . Medical management of HAZMAT victims in civilian practice . Trends in Anaesthesia and Critical Care vol. 9 , ( 2 ) 52 - 57 .

Plaxco KW, Riddle DS, Grantcharova V, Baker D ( 1998 ) . Simplified proteins: minimalist solutions to the ‘protein folding problem’ . Current Opinion in Structural Biology vol. 8 , ( 1 ) 80 - 85 .

Chernajovsky Y, Annenkov A, Herman C, Triantaphyllopoulos K, Gould D, Dreja H, Moyes SP, Croxford JL et al. ( 1998 ) . Gene therapy for rheumatoid arthritis. Theoretical considerations . Drugs and Aging vol. 12 , ( 1 ) 29 - 41 .

Triantaphyllopoulos KA, Croxford JL, Baker D ( 1998 ) . Cloning and expression of murine IFNβ and a TNF antagonist for gene therapy of experimental allergic encephalomyelitis . Gene Therapy vol. 5 , ( 2 ) 253 - 263 .

Ali RR, Reichel MB, Stephens CJ, Thrasher AJ, Hunt DM ( 1998 ) . Co-injection of adenovirus expressing CTLA4-Ig prolongs adenovirally mediated lacZ reporter gene expression in the mouse retina . GENE THERAPY vol. 5 , ( 11 ) 1561 - 1565 .

Reichel MB, Ali RR, Thrasher AJ, Hunt DM ( 1998 ) . Immune responses limit adenovirally mediated gene expression in the adult mouse eye . Gene Therapy vol. 5 , ( 8 ) 1038 - 1046 .

O'Neill JK, Baker D, Morris MM, Gschmeissner SE, Jenkins HG, Kirvell SL ( 1998 ) . Optic neuritis in chronic relapsing experimental allergic encephalomyelitis in Biozzi ABH mice: Demyelination and fast axonal transport changes in disease . JOURNAL OF NEUROIMMUNOLOGY vol. 82 , ( 2 ) 210 - 218 .

Grantcharova VP, Baker D ( 1997 ) . Folding Dynamics of the src SH3 Domain † . Biochemistry vol. 36 , ( 50 ) 15685 - 15692 .

Reichet MB, All RR, Baker D, Byrnes AP, D'Esposito F, Kanuga N, Hunt DM ( 1997 ) . Co-injection of adenovirus expressing CTLA4-IG prolongs adenovirally-mediated lacz reporter gene expression in the mouse retina . Investigative Ophthalmology and Visual Science vol. 38 , ( 4 )

Gu H, Kim D, Baker D ( 1997 ) . Contrasting roles for symmetrically disposed β-turns in the folding of a small protein11Edited by P. E. Wright . Journal of Molecular Biology vol. 274 , ( 4 ) 588 - 596 .

Yi Q, Scalley ML, Simons KT, Gladwin ST, Baker D ( 1997 ) . Characterization of the free energy spectrum of peptostreptococcal protein L . Structure vol. 2 , ( 5 ) 271 - 280 .

Riddle DS, Santiago JV, Bray-Hall ST, Doshi N, Grantcharova VP, Yi Q, Baker D ( 1997 ) . Functional rapidly folding proteins from simplified amino acid sequences . Nature Structural & Molecular Biology vol. 4 , ( 10 ) 805 - 809 .

Scalley ML, Baker D ( 1997 ) . Protein folding kinetics exhibit an Arrhenius temperature dependence when corrected for the temperature dependence of protein stability . Proceedings of the National Academy of Sciences of the United States of America vol. 94 , ( 20 ) 10636 - 10640 .

Thoua NM, van Noort JM, Morris MM, Travers PJ, Amor S ( 1997 ) . The heat shock protein αB-crystallin induces EAE in Blozzi ABH mice . Immunology Letters vol. 56 ,

Simons KT, Kooperberg C, Huang E, Baker D ( 1997 ) . Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and bayesian scoring functions11Edited by F. E. Cohen . Journal of Molecular Biology vol. 268 , ( 1 ) 209 - 225 .

Croxford JL, Baker D ( 1997 ) . Polygenic control of experimental allergic encephalomyelitis in Biozzi ABH and BALB/c mice . J Neuroimmunol vol. 74 , ( 1-2 ) 205 - 211 .

Scalley ML, Yi Q, Gu H, McCormack A, Yates JR, Baker D ( 1997 ) . Kinetics of Folding of the IgG Binding Domain of Peptostreptoccocal Protein L . Biochemistry vol. 36 , ( 11 ) 3373 - 3382 .

Morris MM, Dyson H, Harbige LS ( 1997 ) . Characterization of the cellular and cytokine response in the central nervous system following Semliki Forest virus infection . Journal of Neuroimmunology vol. 74 , ( 1-2 ) 185 - 197 .

Amor S, Baker D, McCormack K, Van Noort JM ( 1997 ) . Multiple sclerosis: Variants on a theme . Immunology Today vol. 18 , ( 8 ) 368 - 371 .

Bolton C, O’ Neill JK, Allen SJ ( 1997 ) . Regulation of Chronic Relapsing Experimental Allergic Encephalomyelitis by Endogenous and Exogenous Glucocorticoids . International Archives of Allergy and Immunology vol. 114 , ( 1 ) 74 - 80 .

Baker DJ ( 1996 ) . Advanced life support for acute toxic injury (TOXALS™) . European Journal of Emergency Medicine vol. 3 , ( 4 ) 256 - 262 .

Bystroff C, Simons KT, Han KF, Baker D ( 1996 ) . Local sequence-structure correlations in proteins . Current Opinion in Biotechnology vol. 7 , ( 4 ) 417 - 421 .

Han KF, Baker D ( 1996 ) . Global properties of the mapping between local amino acid sequence and local structure in proteins . Proceedings of the National Academy of Sciences of the United States of America vol. 93 , ( 12 ) 5814 - 5818 .

Amor S, O'Neill JK, Morris MM, Smith RM, Wraith DC, Baker D ( 1996 ) . Encephalitogenic epitopes of myelin basic protein, proteolipid protein, and myelin oligodendrocyte glycoprotein for experimental allergic encephalomyelitis induction in Biozzi ABH (H-2Ag7) mice share an amino acid motif . Journal of Immunology vol. 156 , ( 8 ) 3000 - 3008 .

Brennan FR, ONeill JK, Allen SJ, Mikecz K ( 1996 ) . Anti-CD44 antibody prevents and ameriolates chronic relapsing experimental allergic encephalomyelitis (CREAE) by inhibition leukocyte migration to the CNS . ARTHRITIS AND RHEUMATISM vol. 39 , ( 9 ) 625 - 625 .

Baker D, Rosenwasser OA ( 1995 ) . Genetic analysis of experimental allergic encephalomyelitis in mice . Journal of Immunology vol. 155 , ( 8 ) 4046 - 4051 .

Han KF, Baker D ( 1995 ) . Recurring Local Sequence Motifs in Proteins . Journal of Molecular Biology vol. 251 , ( 1 ) 176 - 187 .

Amor S, Groome N, Linington C, Dornmair K, Matthieu JM ( 1994 ) . Identification of epitopes of myelin oligodendrocyte glycoprotein for the induction of experimental allergic encephalomyelitis in SJL and Biozzi AB/H mice . The Journal of Immunology vol. 153 , ( 10 ) 4349 - 4356 .

Baker D, Agard DA ( 1994 ) . Influenza hemagglutinin: kinetic control of protein function . Structure vol. 2 , ( 10 ) 907 - 910 .

Lapa-e-Silva JR, Pretolani M, Baker D, Scheper RJ ( 1994 ) . Emergence of T-lymphocytes, eosinophils and dendritic cells in the bronchi of actively sensitized guinea pigs after antigenic challenge . Brazilian Journal of Medical and Biological Research vol. 27 , ( 7 ) 1653 - 1658 .

Baker D, Butler D, Scallon BJ, Turk JL ( 1994 ) . Control of established experimental allergic encephalomyelitis by inhibition of tumor necrosis factor (TNF) activity within the central nervous system using monoclonal antibodies and TNF receptor‐immunoglobulin fusion proteins . European Journal of Immunology vol. 24 , ( 9 ) 2040 - 2048 .

Baker D, Shiau AK, Agard DA ( 1993 ) . The role of pro regions in protein folding . Current Opinion in Cell Biology vol. 5 , ( 6 ) 966 - 970 .

Lapa e Silva JR, Bachelet C-M, Pretolani M, Baker D ( 1993 ) . Immunopathologic Alterations in the Bronchi of Immunized Guinea Pigs . American Journal of Respiratory Cell and Molecular Biology vol. 9 , ( 1 ) 44 - 53 .

Baker D, Chan HS, Dill KA ( 1993 ) . Coordinate-space formulation of polymer lattice cluster theory . The Journal of Chemical Physics vol. 98 , ( 12 ) 9951 - 9962 .

Amor S, Baker D, Turk JL ( 1993 ) . Identification of a major encephalitogenic epitope of proteolipid protein (residues 56-70) for the induction of experimental allergic encephalomyelitis in Biozzi AB/H and nonobese diabetic mice . The Journal of Immunology vol. 150 , ( 12 ) 5666 - 5672 .

Ruohola-Baker H, Grell E, Chou T-B, Baker D, Jan LY, Jan YN ( 1993 ) . Spatially localized rhomboid is required for establishment of the dorsal-ventral axis in Drosophila oogenesis . Cell vol. 73 , ( 5 ) 953 - 965 .

Fairchild S, Turk JL ( 1993 ) . Characterization of experimental allergic encephalomyelitis-susceptible, Biozzi AB/H (H-2dq1) mice which express H-2Anod: analysis of T-cell receptor expression and the detection of a deletion ligand encoded by Mtv-7 . Immunology vol. 78 , ( 2 ) 260 - 265 .

Lapa e Silva J-R, Pretolani M, Bachelet C-M, Shepper RJ ( 1993 ) . Immunohistochemical Characterization of T Lymphocytes and Eosinophils in the Bronchial Wall of Actively Sensitized Guinea Pigs . Chest vol. 103 , ( 2 ) 130s - 132s .

Liu GY, Baker D, Fairchild S, Figueroa F, Quartey-Papafio R, Healey D, Turk JL ( 1993 ) . Complete characterization of the expressed immune response genes in Biozzi AB/H mice: structural and functional identity between AB/H and NOD A region molecules . Immunogenetics vol. 37 , ( 4 ) 296 - 300 .

O'Neill JK, Baker D, Davidson AN, Allen SJ, Butter C ( 1993 ) . Control of immune-mediated disease of the central nervous system with monoclonal (CD4-specific) antibodies . Journal of Neuroimmunology vol. 45 , ( 1-2 ) 1 - 14 .

Preece NE, Baker D, Gadian DG ( 1993 ) . Experimental allergic encephalomyelitis raises betaine levels in the spinal cord of strain 13 guinea-pigs . NMR Biomed vol. 6 , ( 3 ) 194 - 200 .

Allen SJ, Baker D, O’Neill JK, Davison AN ( 1993 ) . Isolation and characterization of cells infiltrating the spinal cord during the course of chronic relapsing experimental allergic encephalomyelitis in the biozzi ab/h mouse . Cellular Immunology vol. 146 , ( 2 ) 335 - 350 .

O'Neill JK, Baker D ( 1992 ) . Inhibition of chronic relapsing experimental allergic encephalomyelitis in the Biozzi AB/H mouse . Journal of Neuroimmunology vol. 41 , ( 2 ) 177 - 187 .

O'Neill JK, Davison AN, Maggon KK, Turk JL ( 1992 ) . Therapy of chronic relapsing experimental allergic encephalomyelitis and the role of the blood-brain barrier: elucidation by the action of Brequinar sodium . Journal of Neuroimmunology vol. 38 , ( 1-2 ) 53 - 62 .

Baker D, Sohl JL, Agard DA ( 1992 ) . A protein-folding reaction under kinetic control . Nature vol. 356 , ( 6366 ) 263 - 265 .

Baker D ( 1991 ) . Mechanisms of immune-mediated demyelinating disease of the central nervous system . Neurochemical Research vol. 16 , ( 9 ) 1067 - 1072 .

Ruohola H, Bremer KA, Baker D, Swedlow JR, Jan LY, Jan YN ( 1991 ) . Role of neurogenic genes in establishment of follicle cell fate and oocyte polarity during oogenesis in Drosophila . Cell vol. 66 , ( 3 ) 433 - 449 .

Butter C, O'Neill JK, Baker D ( 1991 ) . An immunoelectron microscopical study of the expression of class II major histocompatibility complex during chronic relapsing experimental allergic encephalomyelitis in Biozzi AB/H mice . J Neuroimmunol vol. 33 , ( 1 ) 37 - 42 .

Butter C, Baker D, Turk JL ( 1991 ) . Mononuclear cell trafficking and plasma protein extravasation into the CNS during chronic relapsing experimental allergic encephalomyelitis in Biozzi AB/H mice . J Neurol Sci vol. 104 , ( 1 ) 9 - 12 .

Baker D, O'Neill JK, Turk JL ( 1991 ) . Cytokines in the central nervous system of mice during chronic relapsing experimental allergic encephalomyelitis . Cellular Immunology vol. 134 , ( 2 ) 505 - 510 .

O'Neill JK, Butter C, Baker D, Kraal G ( 1991 ) . Expression of vascular addressins and ICAM-1 by endothelial cells in the spinal cord during chronic relapsing experimental allergic encephalomyelitis in the Biozzi AB/H mouse . Immunology vol. 72 , ( 4 ) 520 - 525 .

Yaegashi N, Jenison SA, Valentine JM, Dunn M, Taichman LB, Baker DA, Galloway DA ( 1991 ) . Characterization of murine polyclonal antisera and monoclonal antibodies generated against intact and denatured human papillomavirus type 1 virions . Journal of Virology vol. 65 , ( 3 ) 1578 - 1583 .

Baker D, Kimber I ( 1991 ) . Antigen-specific and non-specific depression of proliferative responses induced during contact sensitivity in mice . International Journal of Experimental Pathology vol. 72 , ( 1 ) 55 - 65 .

Baker D, O'Neill JK, Amor S, Khamashta MA ( 1991 ) . Inhibition of chronic relapsing experimental allergic encephalomyelitis in the mouse by the alkyl-lysophospholipid ET-18-OCH3 . International Journal of Immunopharmacology vol. 13 , ( 4 ) 385 - 392 .

Watson CM, Davison AN, O'Neill JK ( 1991 ) . Suppression of demyelination by mitoxantrone . Int J Immunopharmacol vol. 13 , ( 7 ) 923 - 930 .

Wilcox CE, Ward AM, Evans A, Baker D ( 1990 ) . Endothelial cell expression of the intercellular adhesion molecule-1 (ICAM-1) in the central nervous system of guinea pigs during acute and chronic relapsing experimental allergic encephalomyelitis . J Neuroimmunol vol. 30 , ( 1 ) 43 - 51 .

Baker D, O'Neill JK, Gschmeissner SE, Wilcox CE, Butter C ( 1990 ) . Induction of chronic relapsing experimental allergic encephalomyelitis in Biozzi mice . Journal of Neuroimmunology vol. 28 , ( 3 ) 261 - 270 .

Schäfer H, Baker D, Thiele B ( 1990 ) . Structure, cellular distribution, and functional characteristics of the guinea pig leucocyte common antigen . Cellular Immunology vol. 128 , ( 2 ) 370 - 384 .

Kimber I, Cumberbatch M, Baker D ( 1990 ) . Requirements for antigenic competition in contact sensitivity . Journal of Clinical and Laboratory Immunology vol. 32 , ( 2 ) 67 - 72 .

Baker D, Wuestehube L, Schekman R, Botstein D, Segev N ( 1990 ) . GTP-binding Ypt1 protein and Ca2+ function independently in a cell-free protein transport reaction . Proceedings of the National Academy of Sciences of the United States of America vol. 87 , ( 1 ) 355 - 359 .

Butter C, Healey DG, Baker D ( 1989 ) . A quantitative immunocytochemical study of the infiltrating lymphocytes in the spinal cord of guinea pigs with chronic relapsing experimental allergic encephalomyelitis . J Neuroimmunol vol. 25 , ( 2-3 ) 169 - 176 .

Wilcox CE, Healey DG, Baker D, Turk JL ( 1989 ) . Presentation of myelin basic protein by normal guinea-pig brain endothelial cells and its relevance to experimental allergic encephalomyelitis . Immunology vol. 67 , ( 4 ) 435 - 440 .

Wilcox CE, Baker D, Willoughby DA ( 1989 ) . Differential expression of guinea pig class II major histocompatibility complex antigens on vascular endothelial cells in vitro and in experimental allergic encephalomyelitis . Cell Immunol vol. 120 , ( 1 ) 82 - 91 .

Kimber I, Mitchell JA, Turk JL, Baker D ( 1989 ) . Regulation of lymphocyte proliferation in contact sensitivity: homeostatic mechanisms and a possible explanation of antigenic competition . Immunology vol. 66 , ( 4 ) 577 - 582 .

Baker D, Kimber I ( 1989 ) . Antigen-specific regulation of T lymphocyte proliferative responses to contact-sensitizing chemicals in the guinea pig . Cellular Immunology vol. 119 , ( 1 ) 153 - 159 .

Baker D, Schekman R ( 1989 ) . Chapter 7 Reconstitution of Protein Transport Using Broken Yeast Spheroplasts . Methods in Cell Biology vol. 31 , 127 - 141 .

Kraal G, Shiamatey-Koolma R, Hoffer M ( 1988 ) . Histochemical identification of guinea-pig macrophages by monoclonal antibody MR-1 . Immunology vol. 65 , ( 4 ) 523 - 528 .

Baker D, Hicke L, Rexach M, Schleyer M, Schekman R ( 1988 ) . Reconstitution of SEC gene product-dependent intercompartmental protein transport . Cell vol. 54 , ( 3 ) 335 - 344 .

Payne GS, Baker D, van Tuinen E, Schekman R ( 1988 ) . Protein transport to the vacuole and receptor-mediated endocytosis by clathrin heavy chain-deficient yeast . Journal of Cell Biology vol. 106 , ( 5 ) 1453 - 1461 .

Baker D, Parker D, Healey DG ( 1987 ) . Induction of sensitization and tolerance in contact sensitivity with haptenated epidermal cells in the guinea-pig . Immunology vol. 62 , ( 4 ) 659 - 664 .

Antoniou AV, Baker D, El-Sady E, Tan BTG ( 1987 ) . Identification and quantitation of the expression of T cell surface markers during the development of chronic relapsing experimental allergic encephalomyelitis (CREAE) in the guinea pig . Journal of Neuroimmunology vol. 14 , ( 3 ) 293 - 303 .

BAKER D, PARKER DD, TURK JL ( 1985 ) . Effect of depletion of epidermal dendritic cells on the induction of contact sensitivity in the guinea‐pig . British Journal of Dermatology vol. 113 , ( 3 ) 285 - 294 .

Marta M, Baker D, Creeke P, Pryce G, Gnanapavan S, Giovannoni G . Antigen-specific tolerization in human autoimmunity: Inhibition of interferon-beta1a anti-drug antibodies in multiple sclerosis .

Baker D, MacDougall A, Kang AS, Schmierer K, Giovannoni G, Dobson R . CD19 B cell repopulation after ocrelizumab, alemtuzumab and cladribine: Implications for SARS-CoV-2 vaccinations in multiple sclerosis .

Gnanapavan S, Aboulwafa M, Ammoscato F, Andrews M, Alampritis G, Asardag AN, Baker D, Chance R et al. . COVID-19 exposure risks and protective measures in East London’s healthcare and academic sectors: Insights and applications of GloBody technology for infectious disease monitoring .

Tallantyre EC, Vickaryous N, Anderson V, Asardag AN, Baker D, Bestwick J, Bramhall K, Chance R et al. . COVID-19 vaccine response in people with multiple sclerosis .

Baker D, Roberts C, Pryce G, Kang A, Marta M, Reyes S, Schmierer K, Giovannoni G et al. . COVID-19 vaccine-readiness for ocrelizumab and other anti-CD20-depleting therapies in multiple sclerosis and other autoimmune diseases .

Ammoscato F, Aboulwafa M, Skonieczna J, Bestwick J, Monero R, Andrews M, De Trane S, Holden D et al. . Cladribine tablets in Relapsing-Remitting Multiple Sclerosis preferentially target B-cells .

Allen-Philbey K, Stephenson S, Doody G, MacDougall A, Aboulwafaali M, Ammoscato F, Andrews M, Gnanapavan S et al. . Effects of cladribine on intrathecal and peripheral B and plasma cells .

BAKER D, POSADA CG, SELWOOD D, GARTHWAITE J, CLUTTERBUCK L . Indazole derivatives and their use for blockading voltage gated sodium channels . no. EP20100760746 20100930 ,

Amor S, Blanco LF, Baker D . Innate immunity during SARS-CoV-2: evasion strategies and activation trigger hypoxia and vascular damage .

BAKER D, Turk JL, Feldmann M . Method for treating multiple sclerosis .

Santorella E, Balsbaugh JL, Ge S, Saboori P, Baker D, Pachter JS . Proteomic interrogation of the meninges reveals the molecular identities of structural components and regional distinctions along the CNS axis .

Tallantyre EC, Scurr MJ, Vickaryous N, Richards A, Anderson V, Baker D, Chance R, Evangelou N et al. . Response to COVID-19 booster vaccinations in seronegative people with MS .

Jacobs BM, Taylor T, Awad A, Baker D, Giovanonni G, Noyce A, Dobson R . Summary-data-based mendelian randomisation reveals druggable targets for multiple sclerosis .

Licht-Mayer S, Campbell GR, Mehta AR, McGill K, Symonds A, Al-Azki S, Pryce G, Zhao C et al. . The role of complex IV activity in the axonal response of mitochondria to demyelination in experimental disease models of multiple sclerosis .