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David A. Baker, Ph.D. - Publications

Affiliations: 
Marquette University Marquette University, Milwaukee, WI, United States 
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Year Citation  Score
2018 Vranjkovic O, Van Newenhizen E, Nordness ME, Blacktop JM, Urbanik LA, Mathy JC, McReynolds JR, Miller AM, Doncheck EM, Kloehn TM, Stinnett GS, Gerndt CH, Ketchesin KD, Baker DA, Seasholtz AF, et al. Enhanced CRFR1-dependent regulation of a ventral tegmental area to prelimbic cortex projection establishes susceptibility to stress-induced cocaine seeking. The Journal of Neuroscience : the Official Journal of the Society For Neuroscience. PMID 30355627 DOI: 10.1523/Jneurosci.2080-18.2018  0.454
2017 McReynolds JR, Doncheck EM, Li Y, Vranjkovic O, Graf EN, Ogasawara D, Cravatt BF, Baker DA, Liu QS, Hillard CJ, Mantsch JR. Stress Promotes Drug Seeking Through Glucocorticoid-Dependent Endocannabinoid Mobilization in the Prelimbic Cortex. Biological Psychiatry. PMID 29100630 DOI: 10.1016/J.Biopsych.2017.09.024  0.336
2017 Wheeler DS, Ebben AL, Kurtoglu B, Lovell ME, Bohn AT, Jasek IA, Baker DA, Mantsch JR, Gasser PJ, Wheeler RA. Corticosterone regulates both naturally occurring and cocaine-induced dopamine signaling by selectively decreasing dopamine uptake. The European Journal of Neuroscience. PMID 28965353 DOI: 10.1111/Ejn.13730  0.411
2016 McReynolds JR, Taylor A, Vranjkovic O, Ambrosius T, Derricks O, Nino B, Kurtoglu B, Wheeler RA, Baker DA, Gasser PJ, Mantsch JR. Corticosterone Potentiation of Cocaine-Induced Reinstatement of Conditioned Place Preference in Mice is Mediated by Blockade of the Organic Cation Transporter 3. Neuropsychopharmacology : Official Publication of the American College of Neuropsychopharmacology. PMID 27604564 DOI: 10.1038/Npp.2016.187  0.449
2016 Hsia Y, Bale JB, Gonen S, Shi D, Sheffler W, Fong KK, Nattermann U, Xu C, Huang PS, Ravichandran R, Yi S, Davis TN, Gonen T, King NP, Baker D. Design of a hyperstable 60-subunit protein icosahedron. Nature. PMID 27309817 DOI: 10.1038/Nature18010  0.307
2016 Ovchinnikov S, Park H, Kim DE, Liu Y, Yu-Ruei Wang R, Baker D. Structure Prediction using sparse simulated NOE restraints with Rosetta in CASP11. Proteins. PMID 26857542 DOI: 10.1002/Prot.25006  0.301
2016 Kong L, Albano R, Madayag A, Raddatz N, Mantsch JR, Choi S, Lobner D, Baker DA. Pituitary Adenylate Cyclase-Activating Polypeptide Orchestrates Neuronal Regulation of the Astrocytic Glutamate Releasing Mechanism System xc. Journal of Neurochemistry. PMID 26851652 DOI: 10.1111/Jnc.13566  0.747
2016 Taylor ND, Garruss AS, Moretti R, Chan S, Arbing MA, Cascio D, Rogers JK, Isaacs FJ, Kosuri S, Baker D, Fields S, Church GM, Raman S. Engineering an allosteric transcription factor to respond to new ligands. Nature Methods. 13: 177-83. PMID 26689263 DOI: 10.1038/Nmeth.3696  0.304
2015 Ovchinnikov S, Kim DE, Wang RY, Liu Y, DiMaio F, Baker D. Improved de novo structure prediction in CASP11 by incorporating Co-evolution information into rosetta. Proteins. PMID 26677056 DOI: 10.1002/Prot.24974  0.306
2015 Brunette TJ, Parmeggiani F, Huang PS, Bhabha G, Ekiert DC, Tsutakawa SE, Hura GL, Tainer JA, Baker D. Exploring the repeat protein universe through computational protein design. Nature. PMID 26675729 DOI: 10.1038/Nature16162  0.341
2015 Blacktop JM, Vranjkovic O, Mayer M, Van Hoof M, Baker DA, Mantsch JR. Antagonism of GABA-B but not GABA-A receptors in the VTA prevents stress- and intra-VTA CRF-induced reinstatement of extinguished cocaine seeking in rats. Neuropharmacology. PMID 26596556 DOI: 10.1016/J.Neuropharm.2015.11.013  0.405
2015 Huang PS, Feldmeier K, Parmeggiani F, Fernandez Velasco DA, Höcker B, Baker D. De novo design of a four-fold symmetric TIM-barrel protein with atomic-level accuracy. Nature Chemical Biology. PMID 26595462 DOI: 10.1038/Nchembio.1966  0.308
2015 Bednar D, Beerens K, Sebestova E, Bendl J, Khare S, Chaloupkova R, Prokop Z, Brezovsky J, Baker D, Damborsky J. FireProt: Energy- and Evolution-Based Computational Design of Thermostable Multiple-Point Mutants. Plos Computational Biology. 11: e1004556. PMID 26529612 DOI: 10.1371/Journal.Pcbi.1004556  0.301
2015 McReynolds JR, Doncheck EM, Vranjkovic O, Ganzman GS, Baker DA, Hillard CJ, Mantsch JR. CB1 receptor antagonism blocks stress-potentiated reinstatement of cocaine seeking in rats. Psychopharmacology. PMID 26455361 DOI: 10.1007/S00213-015-4092-X  0.412
2015 Holstein CA, Chevalier A, Bennett S, Anderson CE, Keniston K, Olsen C, Li B, Bales B, Moore DR, Fu E, Baker D, Yager P. Immobilizing affinity proteins to nitrocellulose: a toolbox for paper-based assay developers. Analytical and Bioanalytical Chemistry. PMID 26427504 DOI: 10.1007/S00216-015-9052-0  0.301
2015 Lin YR, Koga N, Tatsumi-Koga R, Liu G, Clouser AF, Montelione GT, Baker D. Control over overall shape and size in de novo designed proteins. Proceedings of the National Academy of Sciences of the United States of America. PMID 26396255 DOI: 10.1073/Pnas.1509508112  0.317
2015 Ovchinnikov S, Kinch L, Park H, Liao Y, Pei J, Kim DE, Kamisetty H, Grishin NV, Baker D. Large scale determination of previously unsolved protein structures using evolutionary information. Elife. 4. PMID 26335199 DOI: 10.7554/Elife.09248  0.325
2015 Park H, DiMaio F, Baker D. CASP11 refinement experiments with ROSETTA. Proteins. PMID 26205421 DOI: 10.1002/Prot.24862  0.311
2015 Bale JB, Park RU, Liu Y, Gonen S, Gonen T, Cascio D, King NP, Yeates TO, Baker D. Structure of a designed tetrahedral protein assembly variant engineered to have improved soluble expression. Protein Science : a Publication of the Protein Society. PMID 26174163 DOI: 10.1002/Pro.2748  0.309
2015 Gonen S, DiMaio F, Gonen T, Baker D. PROTEIN DESIGN. Design of ordered two-dimensional arrays mediated by noncovalent protein-protein interfaces. Science (New York, N.Y.). 348: 1365-8. PMID 26089516 DOI: 10.1126/Science.Aaa9897  0.302
2015 Mantsch JR, Baker DA, Funk D, Lê AD, Shaham Y. Stress-Induced Reinstatement of Drug Seeking: 20 Years of Progress. Neuropsychopharmacology : Official Publication of the American College of Neuropsychopharmacology. PMID 25976297 DOI: 10.1038/Npp.2015.142  0.348
2015 Antala S, Ovchinnikov S, Kamisetty H, Baker D, Dempski RE. Computational modeling and functional studies provide a structural scaffold for the zinc transporter hZIP4. The Journal of Biological Chemistry. PMID 25971965 DOI: 10.1074/Jbc.M114.617613  0.317
2015 Park H, DiMaio F, Baker D. The origin of consistent protein structure refinement from structural averaging. Structure (London, England : 1993). 23: 1123-8. PMID 25960407 DOI: 10.1016/J.Str.2015.03.022  0.302
2015 Pearson AD, Mills JH, Song Y, Nasertorabi F, Han GW, Baker D, Stevens RC, Schultz PG. Transition states. Trapping a transition state in a computationally designed protein bottle. Science (New York, N.Y.). 347: 863-7. PMID 25700516 DOI: 10.1126/Science.Aaa2424  0.303
2015 Park K, Shen BW, Parmeggiani F, Huang PS, Stoddard BL, Baker D. Control of repeat-protein curvature by computational protein design. Nature Structural & Molecular Biology. 22: 167-74. PMID 25580576 DOI: 10.1038/Nsmb.2938  0.308
2015 Parmeggiani F, Huang PS, Vorobiev S, Xiao R, Park K, Caprari S, Su M, Seetharaman J, Mao L, Janjua H, Montelione GT, Hunt J, Baker D. A general computational approach for repeat protein design. Journal of Molecular Biology. 427: 563-75. PMID 25451037 DOI: 10.1016/J.Jmb.2014.11.005  0.317
2015 Rossi P, Shi L, Liu G, Barbieri CM, Lee HW, Grant TD, Luft JR, Xiao R, Acton TB, Snell EH, Montelione GT, Baker D, Lange OF, Sgourakis NG. A hybrid NMR/SAXS-based approach for discriminating oligomeric protein interfaces using Rosetta. Proteins. 83: 309-17. PMID 25388768 DOI: 10.1002/Prot.24719  0.325
2014 Liu DS, Nivón LG, Richter F, Goldman PJ, Deerinck TJ, Yao JZ, Richardson D, Phipps WS, Ye AZ, Ellisman MH, Drennan CL, Baker D, Ting AY. 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. 111: E4551-9. PMID 25313043 DOI: 10.1073/Pnas.1404736111  0.306
2014 Demers JP, Habenstein B, Loquet A, Kumar Vasa S, Giller K, Becker S, Baker D, Lange A, Sgourakis NG. High-resolution structure of the Shigella type-III secretion needle by solid-state NMR and cryo-electron microscopy. Nature Communications. 5: 4976. PMID 25264107 DOI: 10.1038/Ncomms5976  0.308
2014 Vranjkovic O, Gasser PJ, Gerndt CH, Baker DA, Mantsch JR. Stress-induced cocaine seeking requires a beta-2 adrenergic receptor-regulated pathway from the ventral bed nucleus of the stria terminalis that regulates CRF actions in the ventral tegmental area. The Journal of Neuroscience : the Official Journal of the Society For Neuroscience. 34: 12504-14. PMID 25209288 DOI: 10.1523/Jneurosci.0680-14.2014  0.348
2014 Resch JM, Albano R, Liu X, Hjelmhaug J, Lobner D, Baker DA, Choi S. Augmented cystine-glutamate exchange by pituitary adenylate cyclase-activating polypeptide signaling via the VPAC1 receptor. Synapse (New York, N.Y.). PMID 25066643 DOI: 10.1002/Syn.21772  0.304
2014 King NP, Bale JB, Sheffler W, McNamara DE, Gonen S, Gonen T, Yeates TO, Baker D. Accurate design of co-assembling multi-component protein nanomaterials. Nature. 510: 103-8. PMID 24870237 DOI: 10.1038/Nature13404  0.303
2014 Chen KY, Sun J, Salvo JS, Baker D, Barth P. High-resolution modeling of transmembrane helical protein structures from distant homologues. Plos Computational Biology. 10: e1003636. PMID 24854015 DOI: 10.1371/Journal.Pcbi.1003636  0.346
2014 King C, Garza EN, Mazor R, Linehan JL, Pastan I, Pepper M, Baker D. Removing T-cell epitopes with computational protein design. Proceedings of the National Academy of Sciences of the United States of America. 111: 8577-82. PMID 24843166 DOI: 10.1073/Pnas.1321126111  0.303
2014 Ovchinnikov S, Kamisetty H, Baker D. Robust and accurate prediction of residue-residue interactions across protein interfaces using evolutionary information. Elife. 3: e02030. PMID 24842992 DOI: 10.7554/Elife.02030  0.321
2014 Lutgen V, Resch J, Qualmann K, Raddatz NJ, Panhans C, Olander EM, Kong L, Choi S, Mantsch JR, Baker DA. Behavioral assessment of acute inhibition of system xc (-) in rats. Psychopharmacology. 231: 4637-47. PMID 24828877 DOI: 10.1007/S00213-014-3612-4  0.742
2014 McReynolds JR, Vranjkovic O, Thao M, Baker DA, Makky K, Lim Y, Mantsch JR. Beta-2 adrenergic receptors mediate stress-evoked reinstatement of cocaine-induced conditioned place preference and increases in CRF mRNA in the bed nucleus of the stria terminalis in mice. Psychopharmacology. 231: 3953-63. PMID 24696080 DOI: 10.1007/S00213-014-3535-0  0.302
2014 Khoury GA, Liwo A, Khatib F, Zhou H, Chopra G, Bacardit J, Bortot LO, Faccioli RA, Deng X, He Y, Krupa P, Li J, Mozolewska MA, Sieradzan AK, Smadbeck J, ... Baker D, et al. WeFold: a coopetition for protein structure prediction. Proteins. 82: 1850-68. PMID 24677212 DOI: 10.1002/Prot.24538  0.305
2014 Baker D. Protein folding, structure prediction and design Biochemical Society Transactions. 42: 225-229. PMID 24646222 DOI: 10.1042/Bst20130055  0.333
2014 Liu Y, Tan YL, Zhang X, Bhabha G, Ekiert DC, Genereux JC, Cho Y, Kipnis Y, Bjelic S, Baker D, Kelly JW. Small molecule probes to quantify the functional fraction of a specific protein in a cell with minimal folding equilibrium shifts. Proceedings of the National Academy of Sciences of the United States of America. 111: 4449-54. PMID 24591605 DOI: 10.1073/Pnas.1323268111  0.308
2014 Mao B, Tejero R, Baker D, Montelione GT. Protein NMR structures refined with Rosetta have higher accuracy relative to corresponding X-ray crystal structures. Journal of the American Chemical Society. 136: 1893-906. PMID 24392845 DOI: 10.1021/Ja409845W  0.309
2014 Conway P, Tyka MD, DiMaio F, Konerding DE, Baker D. Relaxation of backbone bond geometry improves protein energy landscape modeling. Protein Science : a Publication of the Protein Society. 23: 47-55. PMID 24265211 DOI: 10.1002/Pro.2389  0.311
2014 Kim DE, Dimaio F, Yu-Ruei Wang R, Song Y, Baker D. One contact for every twelve residues allows robust and accurate topology-level protein structure modeling Proteins: Structure, Function and Bioinformatics. 82: 208-218. PMID 23900763 DOI: 10.1002/Prot.24374  0.319
2014 Lutgen V, Kong L, Kau KS, Madayag A, Mantsch JR, Baker DA. Time course of cocaine-induced behavioral and neurochemical plasticity. Addiction Biology. 19: 529-38. PMID 22970924 DOI: 10.1111/J.1369-1600.2012.00493.X  0.78
2014 Terwilliger TC, DiMaio F, Read RJ, Baker D, Brunger AT, Adams PD, Afonine PV, Hung L. Combining Crystallographic and Structure-Modeling Approaches in Macromolecular Crystallography Biophysical Journal. 106: 34a. DOI: 10.1016/J.Bpj.2013.11.263  0.303
2014 Lai Y, King NP, Sheffler W, McNamara DE, Bale JB, Baker D, Yeates TO. Symmetry-Based Design and Structure of Self-Assembling Protein Cages and Nanomaterials Biophysical Journal. 106: 445a. DOI: 10.1016/J.Bpj.2013.11.2516  0.31
2013 Kamisetty H, Ovchinnikov S, Baker D. 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. 110: 15674-15679. PMID 24009338 DOI: 10.1073/Pnas.1314045110  0.31
2013 Tinberg CE, Khare SD, Dou J, Doyle L, Nelson JW, Schena A, Jankowski W, Kalodimos CG, Johnsson K, Stoddard BL, Baker D. Computational design of ligand-binding proteins with high affinity and selectivity. Nature. 501: 212-6. PMID 24005320 DOI: 10.1038/Nature12443  0.301
2013 van der Schot G, Zhang Z, Vernon R, Shen Y, Vranken WF, Baker D, Bonvin AM, Lange OF. Improving 3D structure prediction from chemical shift data. Journal of Biomolecular Nmr. 57: 27-35. PMID 23912841 DOI: 10.1007/S10858-013-9762-6  0.315
2013 Moal IH, Moretti R, Baker D, Fernández-Recio J. Scoring functions for protein-protein interactions. Current Opinion in Structural Biology. 23: 862-7. PMID 23871100 DOI: 10.1016/J.Sbi.2013.06.017  0.328
2013 Graf EN, Wheeler RA, Baker DA, Ebben AL, Hill JE, McReynolds JR, Robble MA, Vranjkovic O, Wheeler DS, Mantsch JR, Gasser PJ. Corticosterone acts in the nucleus accumbens to enhance dopamine signaling and potentiate reinstatement of cocaine seeking. The Journal of Neuroscience : the Official Journal of the Society For Neuroscience. 33: 11800-10. PMID 23864669 DOI: 10.1523/Jneurosci.1969-13.2013  0.367
2013 Procko E, Hedman R, Hamilton K, Seetharaman J, Fleishman SJ, Su M, Aramini J, Kornhaber G, Hunt JF, Tong L, Montelione GT, Baker D. Computational design of a protein-based enzyme inhibitor. Journal of Molecular Biology. 425: 3563-75. PMID 23827138 DOI: 10.1016/J.Jmb.2013.06.035  0.301
2013 Geibel S, Procko E, Hultgren SJ, Baker D, Waksman G. Structural and energetic basis of folded-protein transport by the FimD usher. Nature. 496: 243-6. PMID 23579681 DOI: 10.1038/Nature12007  0.303
2013 Nivón LG, Moretti R, Baker D. A Pareto-optimal refinement method for protein design scaffolds. Plos One. 8: e59004. PMID 23565140 DOI: 10.1371/Journal.Pone.0059004  0.324
2013 Demers JP, Sgourakis NG, Gupta R, Loquet A, Giller K, Riedel D, Laube B, Kolbe M, Baker D, Becker S, Lange A. The common structural architecture of Shigella flexneri and Salmonella typhimurium type three secretion needles. Plos Pathogens. 9: e1003245. PMID 23555258 DOI: 10.1371/Journal.Ppat.1003245  0.306
2013 Lutgen V, Qualmann K, Resch J, Kong L, Choi S, Baker DA. Reduction in phencyclidine induced sensorimotor gating deficits in the rat following increased system xc⁻ activity in the medial prefrontal cortex. Psychopharmacology. 226: 531-40. PMID 23192314 DOI: 10.1007/S00213-012-2926-3  0.738
2012 Koga N, Tatsumi-Koga R, Liu G, Xiao R, Acton TB, Montelione GT, Baker D. Principles for designing ideal protein structures. Nature. 491: 222-7. PMID 23135467 DOI: 10.1038/Nature11600  0.339
2012 Alon A, Grossman I, Gat Y, Kodali VK, DiMaio F, Mehlman T, Haran G, Baker D, Thorpe C, Fass D. The dynamic disulphide relay of quiescin sulphydryl oxidase. Nature. 488: 414-8. PMID 22801504 DOI: 10.1038/Nature11267  0.302
2012 Bridges R, Lutgen V, Lobner D, Baker DA. Thinking outside the cleft to understand synaptic activity: contribution of the cystine-glutamate antiporter (System xc-) to normal and pathological glutamatergic signaling. Pharmacological Reviews. 64: 780-802. PMID 22759795 DOI: 10.1124/Pr.110.003889  0.746
2012 Lange OF, Rossi P, Sgourakis NG, Song Y, Lee HW, Aramini JM, Ertekin A, Xiao R, Acton TB, Montelione GT, Baker D. 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. 109: 10873-8. PMID 22733734 DOI: 10.1073/Pnas.1203013109  0.311
2012 Loquet A, Sgourakis NG, Gupta R, Giller K, Riedel D, Goosmann C, Griesinger C, Kolbe M, Baker D, Becker S, Lange A. Atomic model of the type III secretion system needle Nature. 486: 276-279. PMID 22699623 DOI: 10.1038/Nature11079  0.302
2012 Thompson JM, Sgourakis NG, Liu G, Rossi P, Tang Y, Mills JL, Szyperski T, Montelione GT, Baker D. 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. 109: 9875-80. PMID 22665781 DOI: 10.1073/Pnas.1202485109  0.327
2012 Vranjkovic O, Hang S, Baker DA, Mantsch JR. β-adrenergic receptor mediation of stress-induced reinstatement of extinguished cocaine-induced conditioned place preference in mice: roles for β1 and β2 adrenergic receptors. The Journal of Pharmacology and Experimental Therapeutics. 342: 541-51. PMID 22593095 DOI: 10.1124/Jpet.112.193615  0.322
2012 Fleishman SJ, Baker D. Role of the biomolecular energy gap in protein design, structure, and evolution. Cell. 149: 262-73. PMID 22500796 DOI: 10.1016/J.Cell.2012.03.016  0.306
2012 Thyme SB, Baker D, Bradley P. Improved modeling of side-chain--base interactions and plasticity in protein--DNA interface design. Journal of Molecular Biology. 419: 255-74. PMID 22426128 DOI: 10.1016/J.Jmb.2012.03.005  0.315
2012 Lange OF, Baker D. Resolution-adapted recombination of structural features significantly improves sampling in restraint-guided structure calculation. Proteins. 80: 884-95. PMID 22423358 DOI: 10.1002/Prot.23245  0.311
2012 Rosato A, Aramini JM, Arrowsmith C, Bagaria A, Baker D, Cavalli A, Doreleijers JF, Eletsky A, Giachetti A, Guerry P, Gutmanas A, Güntert P, He Y, Herrmann T, Huang YJ, et al. Blind testing of routine, fully automated determination of protein structures from NMR data. Structure (London, England : 1993). 20: 227-36. PMID 22325772 DOI: 10.1016/J.Str.2012.01.002  0.309
2012 Wojdyla JA, Fleishman SJ, Baker D, Kleanthous C. Structure of the ultra-high-affinity colicin E2 DNase--Im2 complex. Journal of Molecular Biology. 417: 79-94. PMID 22306467 DOI: 10.1016/J.Jmb.2012.01.019  0.334
2012 Handl J, Knowles J, Vernon R, Baker D, Lovell SC. The dual role of fragments in fragment-assembly methods for de novo protein structure prediction. Proteins. 80: 490-504. PMID 22095594 DOI: 10.1002/Prot.23215  0.313
2012 Strauch E, Fleishman SJ, Baker D. De Novo Design of Protein Binders: Targeting Human IgG (Fc) Biophysical Journal. 102: 189a. DOI: 10.1016/J.Bpj.2011.11.1033  0.322
2011 Gilski M, Kazmierczyk M, Krzywda S, Zábranská H, Cooper S, Popović Z, Khatib F, DiMaio F, Thompson J, Baker D, Pichová I, Jaskolski M. High-resolution structure of a retroviral protease folded as a monomer. Acta Crystallographica. Section D, Biological Crystallography. 67: 907-14. PMID 22101816 DOI: 10.1107/S0907444911035943  0.34
2011 Azoitei ML, Correia BE, Ban YE, Carrico C, Kalyuzhniy O, Chen L, Schroeter A, Huang PS, McLellan JS, Kwong PD, Baker D, Strong RK, Schief WR. Computation-guided backbone grafting of a discontinuous motif onto a protein scaffold. Science (New York, N.Y.). 334: 373-6. PMID 22021856 DOI: 10.1126/Science.1209368  0.301
2011 Fleishman SJ, Whitehead TA, Strauch EM, Corn JE, Qin S, Zhou HX, Mitchell JC, Demerdash ON, Takeda-Shitaka M, Terashi G, Moal IH, Li X, Bates PA, Zacharias M, Park H, ... Baker D, et al. Community-wide assessment of protein-interface modeling suggests improvements to design methodology. Journal of Molecular Biology. 414: 289-302. PMID 22001016 DOI: 10.1016/J.Jmb.2011.09.031  0.311
2011 Fleishman SJ, Corn JE, Strauch EM, Whitehead TA, Karanicolas J, Baker D. Hotspot-centric de novo design of protein binders. Journal of Molecular Biology. 413: 1047-62. PMID 21945116 DOI: 10.1016/J.Jmb.2011.09.001  0.304
2011 Khatib F, DiMaio F, Cooper S, Kazmierczyk M, Gilski M, Krzywda S, Zabranska H, Pichova I, Thompson J, Popović Z, Jaskolski M, Baker D. Crystal structure of a monomeric retroviral protease solved by protein folding game players. Nature Structural & Molecular Biology. 18: 1175-7. PMID 21926992 DOI: 10.1038/Nsmb.2119  0.319
2011 Huang PS, Ban YE, Richter F, Andre I, Vernon R, Schief WR, Baker D. RosettaRemodel: a generalized framework for flexible backbone protein design. Plos One. 6: e24109. PMID 21909381 DOI: 10.1371/Journal.Pone.0024109  0.301
2011 Wang RYR, Han Y, Krassovsky K, Sheffler W, Tyka M, Baker D. Modeling disordered regions in proteins using Rosetta Plos One. 6. PMID 21829444 DOI: 10.1371/Journal.Pone.0022060  0.301
2011 Blacktop JM, Seubert C, Baker DA, Ferda N, Lee G, Graf EN, Mantsch JR. Augmented cocaine seeking in response to stress or CRF delivered into the ventral tegmental area following long-access self-administration is mediated by CRF receptor type 1 but not CRF receptor type 2. The Journal of Neuroscience : the Official Journal of the Society For Neuroscience. 31: 11396-403. PMID 21813699 DOI: 10.1523/Jneurosci.1393-11.2011  0.366
2011 DiMaio F, Leaver-Fay A, Bradley P, Baker D, André I. Modeling symmetric macromolecular structures in Rosetta3. Plos One. 6: e20450. PMID 21731614 DOI: 10.1371/Journal.Pone.0020450  0.31
2011 Thompson J, Baker D. Incorporation of evolutionary information into Rosetta comparative modeling. Proteins. 79: 2380-8. PMID 21638331 DOI: 10.1002/Prot.23046  0.33
2011 DiMaio F, Terwilliger TC, Read RJ, Wlodawer A, Oberdorfer G, Wagner U, Valkov E, Alon A, Fass D, Axelrod HL, Das D, Vorobiev SM, Iwaï H, Pokkuluri PR, Baker D. Improved molecular replacement by density- and energy-guided protein structure optimization. Nature. 473: 540-3. PMID 21532589 DOI: 10.1038/Nature09964  0.329
2011 Sgourakis NG, Lange OF, DiMaio F, André I, Fitzkee NC, Rossi P, Montelione GT, Bax A, Baker D. Determination of the structures of symmetric protein oligomers from NMR chemical shifts and residual dipolar couplings. Journal of the American Chemical Society. 133: 6288-98. PMID 21466200 DOI: 10.1021/Ja111318M  0.324
2011 Karanicolas J, Corn JE, Chen I, Joachimiak LA, Dym O, Peck SH, Albeck S, Unger T, Hu W, Liu G, Delbecq S, Montelione GT, Spiegel CP, Liu DR, Baker D. A de novo protein binding pair by computational design and directed evolution. Molecular Cell. 42: 250-60. PMID 21458342 DOI: 10.1016/J.Molcel.2011.03.010  0.319
2011 Fleishman SJ, Khare SD, Koga N, Baker D. Restricted sidechain plasticity in the structures of native proteins and complexes. Protein Science : a Publication of the Protein Society. 20: 753-7. PMID 21432939 DOI: 10.1002/Pro.604  0.324
2011 Kellogg EH, Leaver-Fay A, Baker D. Role of conformational sampling in computing mutation-induced changes in protein structure and stability. Proteins. 79: 830-8. PMID 21287615 DOI: 10.1002/Prot.22921  0.309
2011 Chen DH, Baker ML, Hryc CF, DiMaio F, Jakana J, Wu W, Dougherty M, Haase-Pettingell C, Schmid MF, Jiang W, Baker D, King JA, Chiu W. 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. 108: 1355-60. PMID 21220301 DOI: 10.1073/Pnas.1015739108  0.324
2011 Amen SL, Piacentine LB, Ahmad ME, Li SJ, Mantsch JR, Risinger RC, Baker DA. Repeated N-acetyl cysteine reduces cocaine seeking in rodents and craving in cocaine-dependent humans. Neuropsychopharmacology : Official Publication of the American College of Neuropsychopharmacology. 36: 871-8. PMID 21160464 DOI: 10.1038/Npp.2010.226  0.385
2011 Tyka MD, Keedy DA, André I, Dimaio F, Song Y, Richardson DC, Richardson JS, Baker D. Alternate states of proteins revealed by detailed energy landscape mapping. Journal of Molecular Biology. 405: 607-18. PMID 21073878 DOI: 10.1016/J.Jmb.2010.11.008  0.323
2010 Weerapana E, Wang C, Simon GM, Richter F, Khare S, Dillon MB, Bachovchin DA, Mowen K, Baker D, Cravatt BF. Quantitative reactivity profiling predicts functional cysteines in proteomes. Nature. 468: 790-5. PMID 21085121 DOI: 10.1038/Nature09472  0.311
2010 Tang Y, Schneider WM, Shen Y, Raman S, Inouye M, Baker D, Roth MJ, Montelione GT. Fully automated high-quality NMR structure determination of small (2)H-enriched proteins. Journal of Structural and Functional Genomics. 11: 223-32. PMID 20734145 DOI: 10.1007/S10969-010-9095-6  0.316
2010 Sheffler W, Baker D. RosettaHoles2: A volumetric packing measure for protein structure refinement and validation Protein Science. 19: 1991-1995. PMID 20665689 DOI: 10.1002/Pro.458  0.315
2010 Mantsch JR, Weyer A, Vranjkovic O, Beyer CE, Baker DA, Caretta H. Involvement of noradrenergic neurotransmission in the stress- but not cocaine-induced reinstatement of extinguished cocaine-induced conditioned place preference in mice: role for β-2 adrenergic receptors. Neuropsychopharmacology : Official Publication of the American College of Neuropsychopharmacology. 35: 2165-78. PMID 20613718 DOI: 10.1038/Npp.2010.86  0.36
2010 Meenan NA, Sharma A, Fleishman SJ, Macdonald CJ, Morel B, Boetzel R, Moore GR, Baker D, Kleanthous C. 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. 107: 10080-5. PMID 20479265 DOI: 10.1073/Pnas.0910756107  0.313
2010 Zelter A, Hoopmann MR, Vernon R, Baker D, MacCoss MJ, Davis TN. 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. 9: 3583-3589. PMID 20476776 DOI: 10.1021/Pr1001115  0.308
2010 Raman S, Lange OF, Rossi P, Tyka M, Wang X, Aramini J, Liu G, Ramelot TA, Eletsky A, Szyperski T, Kennedy MA, Prestegard J, Montelione GT, Baker D. NMR structure determination for larger proteins using backbone-only data. Science (New York, N.Y.). 327: 1014-8. PMID 20133520 DOI: 10.1126/Science.1183649  0.309
2010 Wang C, Vernon R, Lange O, Tyka M, Baker D. Prediction of structures of zinc-binding proteins through explicit modeling of metal coordination geometry. Protein Science : a Publication of the Protein Society. 19: 494-506. PMID 20054832 DOI: 10.1002/Pro.327  0.311
2010 Madayag A, Kau KS, Lobner D, Mantsch JR, Wisniewski S, Baker DA. Drug-induced plasticity contributing to heightened relapse susceptibility: neurochemical changes and augmented reinstatement in high-intake rats. The Journal of Neuroscience : the Official Journal of the Society For Neuroscience. 30: 210-7. PMID 20053903 DOI: 10.1523/Jneurosci.1342-09.2010  0.779
2010 Shen Y, Bryan PN, He Y, Orban J, Baker D, Bax A. De novo structure generation using chemical shifts for proteins with high-sequence identity but different folds. Protein Science : a Publication of the Protein Society. 19: 349-56. PMID 19998407 DOI: 10.1002/Pro.303  0.318
2009 Das R, André I, Shen Y, Wu Y, Lemak A, Bansal S, Arrowsmith CH, Szyperski T, Baker D. Simultaneous prediction of protein folding and docking at high resolution. Proceedings of the National Academy of Sciences of the United States of America. 106: 18978-83. PMID 19864631 DOI: 10.1073/Pnas.0904407106  0.317
2009 Kidd BA, Baker D, Thomas WE. Computation of conformational coupling in allosteric proteins. Plos Computational Biology. 5: e1000484. PMID 19714199 DOI: 10.1371/Journal.Pcbi.1000484  0.322
2009 Kim DE, Blum B, Bradley P, Baker D. Sampling bottlenecks in de novo protein structure prediction. Journal of Molecular Biology. 393: 249-60. PMID 19646450 DOI: 10.1016/J.Jmb.2009.07.063  0.321
2009 Havranek JJ, Baker D. Motif-directed flexible backbone design of functional interactions. Protein Science : a Publication of the Protein Society. 18: 1293-305. PMID 19472357 DOI: 10.1002/Pro.142  0.315
2009 Murphy PM, Bolduc JM, Gallaher JL, Stoddard BL, Baker D. Alteration of enzyme specificity by computational loop remodeling and design. Proceedings of the National Academy of Sciences of the United States of America. 106: 9215-20. PMID 19470646 DOI: 10.1073/Pnas.0811070106  0.317
2009 Ashworth J, Baker D. Assessment of the optimization of affinity and specificity at protein-DNA interfaces. Nucleic Acids Research. 37: e73. PMID 19389725 DOI: 10.1093/Nar/Gkp242  0.302
2009 Barth P, Wallner B, Baker D. Prediction of membrane protein structures with complex topologies using limited constraints. Proceedings of the National Academy of Sciences of the United States of America. 106: 1409-14. PMID 19190187 DOI: 10.1073/Pnas.0808323106  0.327
2009 Sheffler W, Baker D. RosettaHoles: Rapid assessment of protein core packing for structure prediction, refinement, design, and validation Protein Science. 18: 229-239. PMID 19177366 DOI: 10.1002/Pro.8  0.312
2009 Shen Y, Vernon R, Baker D, Bax A. De novo protein structure generation from incomplete chemical shift assignments. Journal of Biomolecular Nmr. 43: 63-78. PMID 19034676 DOI: 10.1007/S10858-008-9288-5  0.301
2008 Kau KS, Madayag A, Mantsch JR, Grier MD, Abdulhameed O, Baker DA. Blunted cystine-glutamate antiporter function in the nucleus accumbens promotes cocaine-induced drug seeking. Neuroscience. 155: 530-7. PMID 18601982 DOI: 10.1016/J.Neuroscience.2008.06.010  0.405
2008 Keeble AH, Joachimiak LA, Maté MJ, Meenan N, Kirkpatrick N, Baker D, Kleanthous C. Experimental and computational analyses of the energetic basis for dual recognition of immunity proteins by colicin endonucleases. Journal of Molecular Biology. 379: 745-59. PMID 18471830 DOI: 10.1016/J.Jmb.2008.03.055  0.315
2008 Das R, Baker D. Macromolecular modeling with rosetta. Annual Review of Biochemistry. 77: 363-82. PMID 18410248 DOI: 10.1146/Annurev.Biochem.77.062906.171838  0.318
2008 Shen Y, Lange O, Delaglio F, Rossi P, Aramini JM, Liu G, Eletsky A, Wu Y, Singarapu KK, Lemak A, Ignatchenko A, Arrowsmith CH, Szyperski T, Montelione GT, Baker D, et al. Consistent blind protein structure generation from NMR chemical shift data. Proceedings of the National Academy of Sciences of the United States of America. 105: 4685-90. PMID 18326625 DOI: 10.1073/Pnas.0800256105  0.32
2008 Mantsch JR, Baker DA, Francis DM, Katz ES, Hoks MA, Serge JP. Stressor- and corticotropin releasing factor-induced reinstatement and active stress-related behavioral responses are augmented following long-access cocaine self-administration by rats. Psychopharmacology. 195: 591-603. PMID 17899015 DOI: 10.1007/S00213-007-0950-5  0.349
2008 Baker DA, Madayag A, Kristiansen LV, Meador-Woodruff JH, Haroutunian V, Raju I. Contribution of cystine-glutamate antiporters to the psychotomimetic effects of phencyclidine. Neuropsychopharmacology : Official Publication of the American College of Neuropsychopharmacology. 33: 1760-72. PMID 17728701 DOI: 10.1038/Sj.Npp.1301532  0.764
2008 Mantsch JR, Baker DA, Serge JP, Hoks MA, Francis DM, Katz ES. Surgical adrenalectomy with diurnal corticosterone replacement slows escalation and prevents the augmentation of cocaine-induced reinstatement in rats self-administering cocaine under long-access conditions. Neuropsychopharmacology : Official Publication of the American College of Neuropsychopharmacology. 33: 814-26. PMID 17534378 DOI: 10.1038/Sj.Npp.1301464  0.352
2008 Raman S, Qian B, Baker D, Walker RC. Advances in Rosetta protein structure prediction on massively parallel systems Ibm Journal of Research and Development. 52: 7-18. DOI: 10.1147/Rd.521.0007  0.33
2007 Madayag A, Lobner D, Kau KS, Mantsch JR, Abdulhameed O, Hearing M, Grier MD, Baker DA. Repeated N-acetylcysteine administration alters plasticity-dependent effects of cocaine. The Journal of Neuroscience : the Official Journal of the Society For Neuroscience. 27: 13968-76. PMID 18094234 DOI: 10.1523/Jneurosci.2808-07.2007  0.783
2007 André I, Bradley P, Wang C, Baker D. Prediction of the structure of symmetrical protein assemblies. Proceedings of the National Academy of Sciences of the United States of America. 104: 17656-61. PMID 17978193 DOI: 10.1073/Pnas.0702626104  0.323
2007 Qian B, Raman S, Das R, Bradley P, McCoy AJ, Read RJ, Baker D. High-resolution structure prediction and the crystallographic phase problem. Nature. 450: 259-64. PMID 17934447 DOI: 10.1038/Nature06249  0.32
2007 Barth P, Schonbrun J, Baker D. Toward high-resolution prediction and design of transmembrane helical protein structures. Proceedings of the National Academy of Sciences of the United States of America. 104: 15682-7. PMID 17905872 DOI: 10.1073/Pnas.0702515104  0.317
2007 Wang C, Bradley P, Baker D. Protein-protein docking with backbone flexibility. Journal of Molecular Biology. 373: 503-19. PMID 17825317 DOI: 10.1016/J.Jmb.2007.07.050  0.325
2007 Mantsch JR, Cullinan WE, Tang LC, Baker DA, Katz ES, Hoks MA, Ziegler DR. Daily cocaine self-administration under long-access conditions augments restraint-induced increases in plasma corticosterone and impairs glucocorticoid receptor-mediated negative feedback in rats. Brain Research. 1167: 101-11. PMID 17689506 DOI: 10.1016/J.Brainres.2007.05.080  0.342
2007 Wang C, Schueler-Furman O, Andre I, London N, Fleishman SJ, Bradley P, Qian B, Baker D. RosettaDock in CAPRI rounds 6-12. Proteins. 69: 758-63. PMID 17671979 DOI: 10.1002/Prot.21684  0.338
2007 Malmström L, Riffle M, Strauss CEM, Chivian D, Davis TN, Bonneau R, Baker D. Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology Plos Biology. 5. PMID 17373854 DOI: 10.1371/Journal.Pbio.0050076  0.314
2007 Mantsch JR, Li SJ, Risinger R, Awad S, Katz E, Baker DA, Yang Z. Levo-tetrahydropalmatine attenuates cocaine self-administration and cocaine-induced reinstatement in rats. Psychopharmacology. 192: 581-91. PMID 17361394 DOI: 10.1007/S00213-007-0754-7  0.341
2007 Watters AL, Deka P, Corrent C, Callender D, Varani G, Sosnick T, Baker D. The highly cooperative folding of small naturally occurring proteins is likely the result of natural selection. Cell. 128: 613-24. PMID 17289578 DOI: 10.1016/J.Cell.2006.12.042  0.313
2007 Dantas G, Corrent C, Reichow SL, Havranek JJ, Eletr ZM, Isern NG, Kuhlman B, Varani G, Merritt EA, Baker D. High-resolution structural and thermodynamic analysis of extreme stabilization of human procarboxypeptidase by computational protein design. Journal of Molecular Biology. 366: 1209-21. PMID 17196978 DOI: 10.1016/J.Jmb.2006.11.080  0.323
2007 Wollacott AM, Zanghellini A, Murphy P, Baker D. Prediction of structures of multidomain proteins from structures of the individual domains. Protein Science : a Publication of the Protein Society. 16: 165-75. PMID 17189483 DOI: 10.1110/Ps.062270707  0.313
2006 Baker ML, Jiang W, Wedemeyer WJ, Rixon FJ, Baker D, Chiu W. Ab initio modeling of the herpesvirus VP26 core domain assessed by CryoEM density. Plos Computational Biology. 2: e146. PMID 17069457 DOI: 10.1371/Journal.Pcbi.0020146  0.315
2006 Meiler J, Baker D. ROSETTALIGAND: protein-small molecule docking with full side-chain flexibility. Proteins. 65: 538-48. PMID 16972285 DOI: 10.1002/Prot.21086  0.312
2006 Chivian D, Baker D. Homology modeling using parametric alignment ensemble generation with consensus and energy-based model selection Nucleic Acids Research. 34. PMID 16971460 DOI: 10.1093/Nar/Gkl480  0.308
2006 Dantas G, Watters AL, Lunde BM, Eletr ZM, Isern NG, Roseman T, Lipfert J, Doniach S, Tompa M, Kuhlman B, Stoddard BL, Varani G, Baker D. Mis-translation of a computationally designed protein yields an exceptionally stable homodimer: implications for protein engineering and evolution. Journal of Molecular Biology. 362: 1004-24. PMID 16949611 DOI: 10.1016/J.Jmb.2006.07.092  0.34
2006 Joachimiak LA, Kortemme T, Stoddard BL, Baker D. 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. 361: 195-208. PMID 16831445 DOI: 10.1016/J.Jmb.2006.05.022  0.314
2006 Ashworth J, Havranek JJ, Duarte CM, Sussman D, Monnat RJ, Stoddard BL, Baker D. Computational redesign of endonuclease DNA binding and cleavage specificity. Nature. 441: 656-9. PMID 16738662 DOI: 10.1038/Nature04818  0.301
2006 Dobson N, Dantas G, Baker D, Varani G. High-resolution structural validation of the computational redesign of human U1A protein. Structure (London, England : 1993). 14: 847-56. PMID 16698546 DOI: 10.1016/J.Str.2006.02.011  0.328
2006 Misura KM, Chivian D, Rohl CA, Kim DE, Baker D. 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. 103: 5361-6. PMID 16567638 DOI: 10.1073/Pnas.0509355103  0.302
2006 Arakaki T, Le Trong I, Phizicky E, Quartley E, DeTitta G, Luft J, Lauricella A, Anderson L, Kalyuzhniy O, Worthey E, Myler PJ, Kim D, Baker D, Hol WG, Merritt EA. Structure of Lmaj006129AAA, a hypothetical protein from Leishmania major. Acta Crystallographica. Section F, Structural Biology and Crystallization Communications. 62: 175-9. PMID 16511295 DOI: 10.1107/S1744309106005902  0.318
2006 Baker DA, Kalivas PW. Chapter 1.3 Insights into glutamate physiology: contribution of studies utilizing in vivo microdialysis Handbook of Behavioral Neuroscience. 16: 33-46. DOI: 10.1016/S1569-7339(06)16003-8  0.486
2005 Schueler-Furman O, Wang C, Bradley P, Misura K, Baker D. Progress in modeling of protein structures and interactions. Science (New York, N.Y.). 310: 638-42. PMID 16254179 DOI: 10.1126/Science.1112160  0.304
2005 Cheng G, Qian B, Samudrala R, Baker D. Improvement in protein functional site prediction by distinguishing structural and functional constraints on protein family evolution using computational design. Nucleic Acids Research. 33: 5861-7. PMID 16224101 DOI: 10.1093/Nar/Gki894  0.312
2005 Bradley P, Misura KM, Baker D. Toward high-resolution de novo structure prediction for small proteins. Science (New York, N.Y.). 309: 1868-71. PMID 16166519 DOI: 10.1126/Science.1113801  0.321
2005 Schueler-Furman O, Wang C, Baker D. Progress in protein-protein docking: atomic resolution predictions in the CAPRI experiment using RosettaDock with an improved treatment of side-chain flexibility. Proteins. 60: 187-94. PMID 15981249 DOI: 10.1002/Prot.20556  0.307
2005 Wang C, Schueler-Furman O, Baker D. Improved side-chain modeling for protein-protein docking. Protein Science : a Publication of the Protein Society. 14: 1328-39. PMID 15802647 DOI: 10.1110/Ps.041222905  0.315
2005 Meiler J, Baker D. The fumarate sensor DcuS: progress in rapid protein fold elucidation by combining protein structure prediction methods with NMR spectroscopy. Journal of Magnetic Resonance (San Diego, Calif. : 1997). 173: 310-6. PMID 15780923 DOI: 10.1016/J.Jmr.2004.11.031  0.322
2005 Misura KM, Baker D. Progress and challenges in high-resolution refinement of protein structure models. Proteins. 59: 15-29. PMID 15690346 DOI: 10.1002/Prot.20376  0.325
2005 Saunders CT, Baker D. Recapitulation of protein family divergence using flexible backbone protein design. Journal of Molecular Biology. 346: 631-44. PMID 15670610 DOI: 10.1016/J.Jmb.2004.11.062  0.313
2005 Jiang L, Kuhlman B, Kortemme T, Baker D. A "solvated rotamer" approach to modeling water-mediated hydrogen bonds at protein-protein interfaces. Proteins. 58: 893-904. PMID 15651050 DOI: 10.1002/Prot.20347  0.306
2005 Baker DA, Kalivas PW. Sensitization and relapse dopamine-glutamate interactions Dopamine and Glutamate in Psychiatric Disorders. 355-369. DOI: 10.1007/978-1-59259-852-6_15  0.411
2004 Havranek JJ, Duarte CM, Baker D. A simple physical model for the prediction and design of protein-DNA interactions. Journal of Molecular Biology. 344: 59-70. PMID 15504402 DOI: 10.1016/J.Jmb.2004.09.029  0.312
2004 Misura KM, Morozov AV, Baker D. Analysis of anisotropic side-chain packing in proteins and application to high-resolution structure prediction. Journal of Molecular Biology. 342: 651-64. PMID 15327962 DOI: 10.1016/J.Jmb.2004.07.038  0.329
2004 Kim DE, Chivian D, Baker D. Protein structure prediction and analysis using the Robetta server. Nucleic Acids Research. 32: W526-31. PMID 15215442 DOI: 10.1093/Nar/Gkh468  0.334
2004 Rohl CA, Strauss CE, Chivian D, Baker D. Modeling structurally variable regions in homologous proteins with rosetta. Proteins. 55: 656-77. PMID 15103629 DOI: 10.1002/Prot.10629  0.33
2004 Kuhlman B, Baker D. Exploring folding free energy landscapes using computational protein design. Current Opinion in Structural Biology. 14: 89-95. PMID 15102454 DOI: 10.1016/J.Sbi.2004.01.002  0.332
2004 Watters AL, Baker D. Searching for folded proteins in vitro and in silico. European Journal of Biochemistry / Febs. 271: 1615-22. PMID 15096200 DOI: 10.1111/J.1432-1033.2004.04072.X  0.323
2004 Scalley-Kim M, Baker D. 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. 338: 573-83. PMID 15081814 DOI: 10.1016/J.Jmb.2004.02.055  0.313
2004 Rohl CA, Strauss CE, Misura KM, Baker D. Protein structure prediction using Rosetta. Methods in Enzymology. 383: 66-93. PMID 15063647 DOI: 10.1016/S0076-6879(04)83004-0  0.33
2004 Kortemme T, Baker D. Computational design of protein-protein interactions. Current Opinion in Chemical Biology. 8: 91-7. PMID 15036162 DOI: 10.1016/J.Cbpa.2003.12.008  0.314
2004 Kortemme T, Joachimiak LA, Bullock AN, Schuler AD, Stoddard BL, Baker D. Computational redesign of protein-protein interaction specificity. Nature Structural & Molecular Biology. 11: 371-9. PMID 15034550 DOI: 10.1038/Nsmb749  0.316
2004 Ginalski K, Rychlewski L, Baker D, Grishin NV. 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. 101: 2305-10. PMID 14983005 DOI: 10.1073/Pnas.0306306101  0.313
2004 Kortemme T, Kim DE, Baker D. Computational alanine scanning of protein-protein interfaces. Science's Stke : Signal Transduction Knowledge Environment. 2004: pl2. PMID 14872095 DOI: 10.1126/Stke.2192004Pl2  0.33
2003 Hazbun TR, Malmström L, Anderson S, Graczyk BJ, Fox B, Riffle M, Sundin BA, Aranda JD, McDonald WH, Chiu CH, Snydsman BE, Bradley P, Muller EG, Fields S, Baker D, et al. Assigning function to yeast proteins by integration of technologies. Molecular Cell. 12: 1353-65. PMID 14690591 DOI: 10.1016/S1097-2765(03)00476-3  0.306
2003 Moran MM, Melendez R, Baker D, Kalivas PW, Seamans JK. Cystine/glutamate antiporter regulation of vesicular glutamate release. Annals of the New York Academy of Sciences. 1003: 445-7. PMID 14684484 DOI: 10.1196/Annals.1300.048  0.463
2003 Baker DA, McFarland K, Lake RW, Shen H, Toda S, Kalivas PW. N-acetyl cysteine-induced blockade of cocaine-induced reinstatement. Annals of the New York Academy of Sciences. 1003: 349-51. PMID 14684458 DOI: 10.1196/Annals.1300.023  0.465
2003 Kalivas PW, McFarland K, Bowers S, Szumlinski K, Xi ZX, Baker D. Glutamate transmission and addiction to cocaine. Annals of the New York Academy of Sciences. 1003: 169-75. PMID 14684444 DOI: 10.1196/Annals.1300.009  0.515
2003 Meiler J, Baker D. Rapid protein fold determination using unassigned NMR data. Proceedings of the National Academy of Sciences of the United States of America. 100: 15404-9. PMID 14668443 DOI: 10.1073/Pnas.2434121100  0.322
2003 Kuhlman B, Dantas G, Ireton GC, Varani G, Stoddard BL, Baker D. Design of a novel globular protein fold with atomic-level accuracy. Science (New York, N.Y.). 302: 1364-8. PMID 14631033 DOI: 10.1126/Science.1089427  0.333
2003 Xi ZX, Shen H, Baker DA, Kalivas PW. Inhibition of non-vesicular glutamate release by group III metabotropic glutamate receptors in the nucleus accumbens. Journal of Neurochemistry. 87: 1204-12. PMID 14622100 DOI: 10.1046/J.1471-4159.2003.02093.X  0.412
2003 Chivian D, Kim DE, Malmström L, Bradley P, Robertson T, Murphy P, Strauss CE, Bonneau R, Rohl CA, Baker D. Automated prediction of CASP-5 structures using the Robetta server. Proteins. 53: 524-33. PMID 14579342 DOI: 10.1002/Prot.10529  0.306
2003 Bradley P, Chivian D, Meiler J, Misura KM, Rohl CA, Schief WR, Wedemeyer WJ, Schueler-Furman O, Murphy P, Schonbrun J, Strauss CE, Baker D. Rosetta predictions in CASP5: successes, failures, and prospects for complete automation. Proteins. 53: 457-68. PMID 14579334 DOI: 10.1002/Prot.10552  0.315
2003 Meiler J, Baker D. Coupled prediction of protein secondary and tertiary structure. Proceedings of the National Academy of Sciences of the United States of America. 100: 12105-10. PMID 14528006 DOI: 10.1073/Pnas.1831973100  0.302
2003 Sadreyev RI, Baker D, Grishin NV. Profile-profile comparisons by COMPASS predict intricate homologies between protein families. Protein Science : a Publication of the Protein Society. 12: 2262-72. PMID 14500884 DOI: 10.1110/Ps.03197403  0.312
2003 Dantas G, Kuhlman B, Callender D, Wong M, Baker D. A large scale test of computational protein design: folding and stability of nine completely redesigned globular proteins. Journal of Molecular Biology. 332: 449-60. PMID 12948494 DOI: 10.1016/S0022-2836(03)00888-X  0.333
2003 Tsai J, Bonneau R, Morozov AV, Kuhlman B, Rohl CA, Baker D. An improved protein decoy set for testing energy functions for protein structure prediction. Proteins. 53: 76-87. PMID 12945051 DOI: 10.1002/Prot.10454  0.317
2003 Ivankov DN, Garbuzynskiy SO, Alm E, Plaxco KW, Baker D, Finkelstein AV. Contact order revisited: influence of protein size on the folding rate. Protein Science : a Publication of the Protein Society. 12: 2057-62. PMID 12931003 DOI: 10.1110/Ps.0302503  0.301
2003 Gray JJ, Moughon S, Wang C, Schueler-Furman O, Kuhlman B, Rohl CA, Baker D. Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations. Journal of Molecular Biology. 331: 281-99. PMID 12875852 DOI: 10.1016/S0022-2836(03)00670-3  0.331
2003 Kinch LN, Baker D, Grishin NV. Deciphering a novel thioredoxin-like fold family. Proteins. 52: 323-31. PMID 12866046 DOI: 10.1002/Prot.10425  0.31
2003 Schueler-Furman O, Baker D. Conserved residue clustering and protein structure prediction. Proteins. 52: 225-35. PMID 12833546 DOI: 10.1002/Prot.10365  0.312
2003 Baker DA, McFarland K, Lake RW, Shen H, Tang XC, Toda S, Kalivas PW. Neuroadaptations in cystine-glutamate exchange underlie cocaine relapse. Nature Neuroscience. 6: 743-9. PMID 12778052 DOI: 10.1038/Nn1069  0.507
2003 Petzold A, Baker D, Pryce G, Keir G, Thompson EJ, Giovannoni G. Quantification of neurodegeneration by measurement of brain-specific proteins. Journal of Neuroimmunology. 138: 45-8. PMID 12742652 DOI: 10.1016/S0165-5728(03)00092-4  0.306
2003 Chivian D, Robertson T, Bonneau R, Baker D. Ab initio methods Methods of Biochemical Analysis. 44: 547-557. PMID 12647404 DOI: 10.1002/0471721204.Ch27  0.301
2003 Kortemme T, Morozov AV, Baker D. An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes. Journal of Molecular Biology. 326: 1239-59. PMID 12589766 DOI: 10.1016/S0022-2836(03)00021-4  0.307
2003 Kalivas PW, Toda S, Bowers MS, Baker DA, Ghasemzadeh MB. The temporal sequence of changes in gene expression by drugs of abuse. Methods in Molecular Medicine. 79: 3-11. PMID 12506686 DOI: 10.1385/1-59259-358-5:03  0.36
2002 Baker D. Progress in AB Initio Protein Structure Prediction. The Scientific World Journal. 2: 31-31. PMID 29973789 DOI: 10.1100/Tsw.2002.15  0.342
2002 Nauli S, Kuhlman B, Le Trong I, Stenkamp RE, Teller D, Baker D. Crystal structures and increased stabilization of the protein G variants with switched folding pathways NuG1 and NuG2. Protein Science : a Publication of the Protein Society. 11: 2924-31. PMID 12441390 DOI: 10.1110/Ps.0216902  0.317
2002 Chevalier BS, Kortemme T, Chadsey MS, Baker D, Monnat RJ, Stoddard BL. Design, activity, and structure of a highly specific artificial endonuclease. Molecular Cell. 10: 895-905. PMID 12419232 DOI: 10.1016/S1097-2765(02)00690-1  0.312
2002 Xi ZX, Ramamoorthy S, Baker DA, Shen H, Samuvel DJ, Kalivas PW. Modulation of group II metabotropic glutamate receptor signaling by chronic cocaine. The Journal of Pharmacology and Experimental Therapeutics. 303: 608-15. PMID 12388642 DOI: 10.1124/Jpet.102.039735  0.566
2002 Baker DA, Xi ZX, Shen H, Swanson CJ, Kalivas PW. The origin and neuronal function of in vivo nonsynaptic glutamate. The Journal of Neuroscience : the Official Journal of the Society For Neuroscience. 22: 9134-41. PMID 12388621 DOI: 10.1523/Jneurosci.22-20-09134.2002  0.654
2002 Kortemme T, Baker D. 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. 99: 14116-21. PMID 12381794 DOI: 10.1073/Pnas.202485799  0.318
2002 Baker DA, Shen H, Kalivas PW. Cystine/glutamate exchange serves as the source for extracellular glutamate: modifications by repeated cocaine administration. Amino Acids. 23: 161-2. PMID 12373531 DOI: 10.1007/s00726-001-0122-6  0.499
2002 Alm E, Morozov AV, Kortemme T, Baker D. Simple physical models connect theory and experiment in protein folding kinetics. Journal of Molecular Biology. 322: 463-76. PMID 12217703 DOI: 10.1016/S0022-2836(02)00706-4  0.316
2002 Bonneau R, Strauss CE, Rohl CA, Chivian D, Bradley P, Malmström L, Robertson T, Baker D. De novo prediction of three-dimensional structures for major protein families. Journal of Molecular Biology. 322: 65-78. PMID 12215415 DOI: 10.1016/S0022-2836(02)00698-8  0.325
2002 Bonneau R, Ruczinski I, Tsai J, Baker D. Contact order and ab initio protein structure prediction. Protein Science : a Publication of the Protein Society. 11: 1937-44. PMID 12142448 DOI: 10.1110/Ps.3790102  0.323
2002 Schonbrun J, Wedemeyer WJ, Baker D. Protein structure prediction in 2002. Current Opinion in Structural Biology. 12: 348-54. PMID 12127454 DOI: 10.1016/S0959-440X(02)00336-6  0.318
2002 Ruczinski I, Kooperberg C, Bonneau R, Baker D. Distributions of beta sheets in proteins with application to structure prediction Proteins: Structure, Function and Genetics. 48: 85-97. PMID 12012340 DOI: 10.1002/Prot.10123  0.308
2002 Walters CE, Pryce G, Hankey DJ, Sebti SM, Hamilton AD, Baker D, Greenwood J, Adamson P. 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. Journal of Immunology (Baltimore, Md. : 1950). 168: 4087-94. PMID 11937568 DOI: 10.4049/Jimmunol.168.8.4087  0.307
2002 Rohl CA, Baker D. De novo determination of protein backbone structure from residual dipolar couplings using Rosetta. Journal of the American Chemical Society. 124: 2723-9. PMID 11890823 DOI: 10.1021/Ja016880E  0.338
2002 Larson SM, Ruczinski I, Davidson AR, Baker D, Plaxco KW. Residues participating in the protein folding nucleus do not exhibit preferential evolutionary conservation. Journal of Molecular Biology. 316: 225-33. PMID 11851333 DOI: 10.1006/Jmbi.2001.5344  0.322
2002 Kuhlman B, O'Neill JW, Kim DE, Zhang KY, Baker D. Accurate computer-based design of a new backbone conformation in the second turn of protein L. Journal of Molecular Biology. 315: 471-7. PMID 11786026 DOI: 10.1006/Jmbi.2001.5229  0.315
2002 Xi ZX, Baker DA, Shen H, Carson DS, Kalivas PW. Group II metabotropic glutamate receptors modulate extracellular glutamate in the nucleus accumbens. The Journal of Pharmacology and Experimental Therapeutics. 300: 162-71. PMID 11752112 DOI: 10.1124/Jpet.300.1.162  0.49
2001 Bonneau R, Tsai J, Ruczinski I, Chivian D, Rohl C, Strauss CE, Baker D. Rosetta in CASP4: progress in ab initio protein structure prediction. Proteins. 119-26. PMID 11835488 DOI: 10.1002/Prot.1170  0.32
2001 Lee MR, Tsai J, Baker D, Kollman PA. Molecular dynamics in the endgame of protein structure prediction. Journal of Molecular Biology. 313: 417-30. PMID 11800566 DOI: 10.1006/Jmbi.2001.5032  0.318
2001 Swanson CJ, Baker DA, Carson D, Worley PF, Kalivas PW. Repeated cocaine administration attenuates group I metabotropic glutamate receptor-mediated glutamate release and behavioral activation: a potential role for Homer. The Journal of Neuroscience : the Official Journal of the Society For Neuroscience. 21: 9043-52. PMID 11698615 DOI: 10.1523/Jneurosci.21-22-09043.2001  0.702
2001 Baker D, Sali A. Protein Structure Prediction and Structural Genomics Science. 294: 93-96. PMID 11588250 DOI: 10.1126/Science.1065659  0.32
2001 Bonneau R, Tsai J, Ruczinski I, Baker D. Functional inferences from blind ab initio protein structure predictions. Journal of Structural Biology. 134: 186-90. PMID 11551178 DOI: 10.1006/Jsbi.2000.4370  0.314
2001 Nauli S, Kuhlman B, Baker D. Computer-based redesign of a protein folding pathway. Nature Structural Biology. 8: 602-5. PMID 11427890 DOI: 10.1038/89638  0.308
2001 Baker DA, Tran-Nguyen TL, Fuchs RA, Neisewander JL. Influence of individual differences and chronic fluoxetine treatment on cocaine-seeking behavior in rats. Psychopharmacology. 155: 18-26. PMID 11374332 DOI: 10.1007/S002130000676  0.752
2001 O'Neill JW, Kim DE, Baker D, Zhang KY. Structures of the B1 domain of protein L from Peptostreptococcus magnus with a tyrosine to tryptophan substitution. Acta Crystallographica. Section D, Biological Crystallography. 57: 480-7. PMID 11264576 DOI: 10.1107/S0907444901000373  0.311
2001 Simons KT, Strauss C, Baker D. Prospects for ab initio protein structural genomics. Journal of Molecular Biology. 306: 1191-9. PMID 11237627 DOI: 10.1006/Jmbi.2000.4459  0.339
2001 Grantcharova V, Alm EJ, Baker D, Horwich AL. Mechanisms of protein folding. Current Opinion in Structural Biology. 11: 70-82. PMID 11179895 DOI: 10.1016/S0959-440X(00)00176-7  0.313
2000 Bowers PM, Strauss CE, Baker D. De novo protein structure determination using sparse NMR data. Journal of Biomolecular Nmr. 18: 311-8. PMID 11200525 DOI: 10.1023/A:1026744431105  0.33
2000 Plaxco KW, Simons KT, Ruczinski I, Baker D. Topology, stability, sequence, and length: defining the determinants of two-state protein folding kinetics. Biochemistry. 39: 11177-83. PMID 10985762 DOI: 10.1021/Bi000200N  0.328
2000 McCallister EL, Alm E, Baker D. Critical role of β-hairpin formation in protein G folding Nature Structural Biology. 7: 669-673. PMID 10932252 DOI: 10.1038/77971  0.303
2000 Bystroff C, Thorsson V, Baker D. HMMSTR: a hidden Markov model for local sequence-structure correlations in proteins. Journal of Molecular Biology. 301: 173-90. PMID 10926500 DOI: 10.1006/Jmbi.2000.3837  0.318
2000 Baker D. A surprising simplicity to protein folding. Nature. 405: 39-42. PMID 10811210 DOI: 10.1038/35011000  0.327
2000 Plaxco KW, Larson S, Ruczinski I, Riddle DS, Thayer EC, Buchwitz B, Davidson AR, Baker D. Evolutionary conservation in protein folding kinetics. Journal of Molecular Biology. 298: 303-12. PMID 10764599 DOI: 10.1006/Jmbi.1999.3663  0.308
2000 Neisewander JL, Baker DA, Fuchs RA, Tran-Nguyen LT, Palmer A, Marshall JF. Fos protein expression and cocaine-seeking behavior in rats after exposure to a cocaine self-administration environment. The Journal of Neuroscience : the Official Journal of the Society For Neuroscience. 20: 798-805. PMID 10632609 DOI: 10.1523/Jneurosci.20-02-00798.2000  0.753
1999 Alm E, Baker D. 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. 96: 11305-10. PMID 10500172 DOI: 10.1073/Pnas.96.20.11305  0.311
1999 Tran-Nguyen LT, Baker DA, Grote KA, Solano J, Neisewander JL. Serotonin depletion attenuates cocaine-seeking behavior in rats. Psychopharmacology. 146: 60-6. PMID 10485965 DOI: 10.1007/S002130051088  0.616
1999 Baker DA, Fuchs RA, Tran-Nguyen LT, Palmer AJ, Marshall JF, McPherson RJ, Neisewander JL. Cocaine-seeking behavior and Fos expression in the amygdala produced by cocaine or a cocaine self-administration environment. Annals of the New York Academy of Sciences. 877: 796-9. PMID 10415707 DOI: 10.1111/J.1749-6632.1999.Tb09325.X  0.746
1999 Simons KT, Ruczinski I, Kooperberg C, Fox BA, Bystroff C, Baker D. Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins. Proteins. 34: 82-95. PMID 10336385 DOI: 10.1002/(Sici)1097-0134(19990101)34:1<82::Aid-Prot7>3.0.Co;2-A  0.308
1999 Alm E, Baker D. Matching theory and experiment in protein folding. Current Opinion in Structural Biology. 9: 189-96. PMID 10322214 DOI: 10.1016/S0959-440X(99)80027-X  0.324
1999 Simons KT, Bonneau R, Ruczinski I, Baker D. Ab initio protein structure prediction of CASP III targets using ROSETTA Proteins: Structure, Function, and Genetics. 37: 171-176. DOI: 10.1002/(Sici)1097-0134(1999)37:3+<171::Aid-Prot21>3.0.Co;2-Z  0.316
1998 Kim DE, Yi Q, Gladwin ST, Goldberg JM, Baker D. The single helix in protein L is largely disrupted at the rate-limiting step in folding. Journal of Molecular Biology. 284: 807-15. PMID 9826517 DOI: 10.1006/Jmbi.1998.2200  0.305
1998 Khroyan TV, Baker DA, Fuchs RA, Manders N, Neisewander JL. Differential effects of 7-OH-DPAT on amphetamine-induced stereotypy and conditioned place preference. Psychopharmacology. 139: 332-41. PMID 9809854 DOI: 10.1007/S002130050724  0.727
1998 Shortle D, Simons KT, Baker D. 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. 95: 11158-62. PMID 9736706 DOI: 10.1073/Pnas.95.19.11158  0.319
1998 Baker DA, Fuchs RA, Specio SE, Khroyan TV, Neisewander JL. Effects of intraaccumbens administration of SCH-23390 on cocaine-induced locomotion and conditioned place preference. Synapse (New York, N.Y.). 30: 181-93. PMID 9723788 DOI: 10.1002/(Sici)1098-2396(199810)30:2<181::Aid-Syn8>3.0.Co;2-8  0.753
1998 Baker DA, Specio SE, Tran-Nguyen LT, Neisewander JL. Amphetamine infused into the ventrolateral striatum produces oral stereotypies and conditioned place preference. Pharmacology, Biochemistry, and Behavior. 61: 107-11. PMID 9715812 DOI: 10.1016/S0091-3057(98)00070-7  0.595
1998 Bystroff C, Baker D. Prediction of local structure in proteins using a library of sequence-structure motifs. Journal of Molecular Biology. 281: 565-77. PMID 9698570 DOI: 10.1006/Jmbi.1998.1943  0.301
1998 Tran-Nguyen LT, Fuchs RA, Coffey GP, Baker DA, O'Dell LE, Neisewander JL. Time-dependent changes in cocaine-seeking behavior and extracellular dopamine levels in the amygdala during cocaine withdrawal. Neuropsychopharmacology : Official Publication of the American College of Neuropsychopharmacology. 19: 48-59. PMID 9608576 DOI: 10.1016/S0893-133X(97)00205-4  0.789
1998 Kim DE, Gu H, Baker D. 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. 95: 4982-6. PMID 9560214 DOI: 10.1073/Pnas.95.9.4982  0.314
1998 Plaxco KW, Riddle DS, Grantcharova V, Baker D. Simplified proteins: minimalist solutions to the 'protein folding problem'. Current Opinion in Structural Biology. 8: 80-5. PMID 9519299 DOI: 10.1016/S0959-440X(98)80013-4  0.321
1997 Khroyan TV, Fuchs RA, Baker DA, Neisewander JL. Effects of D3-preferring agonists 7-OH-PIPAT and PD-128,907 on motor behaviors and place conditioning. Behavioural Pharmacology. 8: 65-74. PMID 9833002 DOI: 10.1097/00008877-199702000-00007  0.71
1997 Riddle DS, Santiago JV, Bray-Hall ST, Doshi N, Grantcharova VP, Yi Q, Baker D. Functional rapidly folding proteins from simplified amino acid sequences. Nature Structural Biology. 4: 805-9. PMID 9334745 DOI: 10.1038/Nsb1097-805  0.313
1997 Simons KT, Kooperberg C, Huang E, Baker D. Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. Journal of Molecular Biology. 268: 209-25. PMID 9149153 DOI: 10.1006/Jmbi.1997.0959  0.315
1996 Baker DA, Khroyan TV, O'Dell LE, Fuchs RA, Neisewander JL. Differential effects of intra-accumbens sulpiride on cocaine-induced locomotion and conditioned place preference. The Journal of Pharmacology and Experimental Therapeutics. 279: 392-401. PMID 8859018  0.792
1995 Khroyan TV, Baker DA, Neisewander JL. Dose-dependent effects of the D3-preferring agonist 7-OH-DPAT on motor behaviors and place conditioning. Psychopharmacology. 122: 351-7. PMID 8657832 DOI: 10.1007/Bf02246265  0.579
1995 Gu H, Yi Q, Bray ST, Riddle DS, Shiau AK, Baker D. A phage display system for studying the sequence determinants of protein folding. Protein Science : a Publication of the Protein Society. 4: 1108-17. PMID 7549875 DOI: 10.1002/Pro.5560040609  0.301
1994 Baker D, Agard DA. Kinetics versus thermodynamics in protein folding. Biochemistry. 33: 7505-9. PMID 8011615 DOI: 10.1021/Bi00190A002  0.308
Low-probability matches (unlikely to be authored by this person)
2009 Rosato A, Bagaria A, Baker D, Bardiaux B, Cavalli A, Doreleijers JF, Giachetti A, Guerry P, Güntert P, Herrmann T, Huang YJ, Jonker HR, Mao B, Malliavin TE, Montelione GT, et al. CASD-NMR: critical assessment of automated structure determination by NMR. Nature Methods. 6: 625-6. PMID 19718014 DOI: 10.1038/Nmeth0909-625  0.3
2013 Kiss G, Çelebi-Ölçüm N, Moretti R, Baker D, Houk KN. Computational enzyme design. Angewandte Chemie (International Ed. in English). 52: 5700-25. PMID 23526810 DOI: 10.1002/Anie.201204077  0.3
2011 Fleishman SJ, Leaver-Fay A, Corn JE, Strauch EM, Khare SD, Koga N, Ashworth J, Murphy P, Richter F, Lemmon G, Meiler J, Baker D. RosettaScripts: a scripting language interface to the Rosetta macromolecular modeling suite. Plos One. 6: e20161. PMID 21731610 DOI: 10.1371/Journal.Pone.0020161  0.3
2005 Lacy DB, Lin HC, Melnyk RA, Schueler-Furman O, Reither L, Cunningham K, Baker D, Collier RJ. A model of anthrax toxin lethal factor bound to protective antigen. Proceedings of the National Academy of Sciences of the United States of America. 102: 16409-14. PMID 16251269 DOI: 10.1073/Pnas.0508259102  0.3
2001 Minard P, Scalley-Kim M, Watters A, Baker D. A "loop entropy reduction" phage-display selection for folded amino acid sequences. Protein Science : a Publication of the Protein Society. 10: 129-34. PMID 11266601 DOI: 10.1110/Ps.32401  0.299
2005 Bradley P, Malmström L, Qian B, Schonbrun J, Chivian D, Kim DE, Meiler J, Misura KM, Baker D. Free modeling with Rosetta in CASP6. Proteins. 61: 128-34. PMID 16187354 DOI: 10.1002/Prot.20729  0.299
2005 Morozov AV, Havranek JJ, Baker D, Siggia ED. Protein-DNA binding specificity predictions with structural models. Nucleic Acids Research. 33: 5781-98. PMID 16246914 DOI: 10.1093/Nar/Gki875  0.299
2010 Raman S, Huang YJ, Mao B, Rossi P, Aramini JM, Liu G, Montelione GT, Baker D. Accurate automated protein NMR structure determination using unassigned NOESY data. Journal of the American Chemical Society. 132: 202-7. PMID 20000319 DOI: 10.1021/Ja905934C  0.299
2011 Warner LR, Varga K, Lange OF, Baker SL, Baker D, Sousa MC, Pardi A. Structure of the BamC two-domain protein obtained by Rosetta with a limited NMR data set. Journal of Molecular Biology. 411: 83-95. PMID 21624375 DOI: 10.1016/J.Jmb.2011.05.022  0.298
2006 Yarov-Yarovoy V, Schonbrun J, Baker D. Multipass membrane protein structure prediction using Rosetta. Proteins. 62: 1010-25. PMID 16372357 DOI: 10.1002/Prot.20817  0.298
1996 Han KF, Baker D. 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. 93: 5814-8. PMID 8650175 DOI: 10.1073/Pnas.93.12.5814  0.298
2011 Brzovic PS, Heikaus CC, Kisselev L, Vernon R, Herbig E, Pacheco D, Warfield L, Littlefield P, Baker D, Klevit RE, Hahn S. The acidic transcription activator Gcn4 binds the mediator subunit Gal11/Med15 using a simple protein interface forming a fuzzy complex. Molecular Cell. 44: 942-53. PMID 22195967 DOI: 10.1016/J.Molcel.2011.11.008  0.298
2010 Blum B, Jordan MI, Baker D. Feature space resampling for protein conformational search. Proteins. 78: 1583-93. PMID 20131376 DOI: 10.1002/Prot.22677  0.298
2015 Blok NB, Tan D, Wang RY, Penczek PA, Baker D, DiMaio F, Rapoport TA, Walz T. 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. PMID 26170309 DOI: 10.1073/Pnas.1500257112  0.298
2003 Gray JJ, Moughon SE, Kortemme T, Schueler-Furman O, Misura KM, Morozov AV, Baker D. Protein-protein docking predictions for the CAPRI experiment. Proteins. 52: 118-22. PMID 12784377 DOI: 10.1002/Prot.10384  0.298
2015 Smith RD, Damm-Ganamet KL, Dunbar JB, Ahmed A, Chinnaswamy K, Delproposto JE, Kubish GM, Tinberg CE, Khare SD, Dou J, Doyle L, Stuckey JA, Baker D, Carlson HA. CSAR Benchmark Exercise 2013: Evaluation of Results from a Combined Computational Protein Design, Docking, and Scoring/Ranking Challenge. Journal of Chemical Information and Modeling. PMID 26419257 DOI: 10.1021/Acs.Jcim.5B00387  0.297
2013 Fang J, Mehlich A, Koga N, Huang J, Koga R, Gao X, Hu C, Jin C, Rief M, Kast J, Baker D, Li H. Forced protein unfolding leads to highly elastic and tough protein hydrogels. Nature Communications. 4: 2974. PMID 24352111 DOI: 10.1038/Ncomms3974  0.297
2010 Fowler DM, Araya CL, Fleishman SJ, Kellogg EH, Stephany JJ, Baker D, Fields S. High-resolution mapping of protein sequence-function relationships. Nature Methods. 7: 741-6. PMID 20711194 DOI: 10.1038/Nmeth.1492  0.297
1997 Doyle R, Simons K, Qian H, Baker D. Local interactions and the optimization of protein folding. Proteins. 29: 282-91. PMID 9365984 DOI: 10.1002/(Sici)1097-0134(199711)29:3<282::Aid-Prot3>3.0.Co;2-D  0.297
2011 Korzhnev DM, Vernon RM, Religa TL, Hansen AL, Baker D, Fersht AR, Kay LE. 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. 133: 10974-82. PMID 21639149 DOI: 10.1021/Ja203686T  0.297
2009 Raman S, Vernon R, Thompson J, Tyka M, Sadreyev R, Pei J, Kim D, Kellogg E, DiMaio F, Lange O, Kinch L, Sheffler W, Kim BH, Das R, Grishin NV, Baker D, et al. Structure prediction for CASP8 with all-atom refinement using Rosetta. Proteins. 77: 89-99. PMID 19701941 DOI: 10.1002/Prot.22540  0.297
2014 Thyme S, Baker D. Redesigning the specificity of protein-DNA interactions with rosetta Methods in Molecular Biology. 1123: 265-282. PMID 24510272 DOI: 10.1007/978-1-62703-968-0_17  0.297
2014 Nivón LG, Bjelic S, King C, Baker D. Automating human intuition for protein design. Proteins. 82: 858-66. PMID 24265170 DOI: 10.1002/Prot.24463  0.296
2000 Kuhlman B, Baker D. Native protein sequences are close to optimal for their structures. Proceedings of the National Academy of Sciences of the United States of America. 97: 10383-8. PMID 10984534 DOI: 10.1073/Pnas.97.19.10383  0.296
2019 Cannon KA, Park RU, Boyken SE, Nattermann U, Yi S, Baker D, King NP, Yeates TO. Design and structure of two new protein cages illustrate successes and ongoing challenges in protein engineeringfig. Protein Science : a Publication of the Protein Society. PMID 31840320 DOI: 10.1002/Pro.3802  0.296
2015 Heinisch T, Pellizzoni M, Dürrenberger M, Tinberg CE, Köhler V, Klehr J, Häussinger D, Baker D, Ward TR. Improving the Catalytic Performance of an Artificial Metalloenzyme by Computational Design. Journal of the American Chemical Society. 137: 10414-9. PMID 26226626 DOI: 10.1021/Jacs.5B06622  0.296
2009 Das R, Baker D. Prospects for de novo phasing with de novo protein models. Acta Crystallographica. Section D, Biological Crystallography. 65: 169-75. PMID 19171972 DOI: 10.1107/S0907444908020039  0.295
2015 Albano R, Raddatz NJ, Hjelmhaug J, Baker DA, Lobner D. Regulation of System x c (-) by Pharmacological Manipulation of Cellular Thiols. Oxidative Medicine and Cellular Longevity. 2015: 269371. PMID 25949770 DOI: 10.1155/2015/269371  0.295
2014 Rajagopalan S, Wang C, Yu K, Kuzin AP, Richter F, Lew S, Miklos AE, Matthews ML, Seetharaman J, Su M, Hunt JF, Cravatt BF, Baker D. Design of activated serine-containing catalytic triads with atomic-level accuracy. Nature Chemical Biology. 10: 386-91. PMID 24705591 DOI: 10.1038/Nchembio.1498  0.295
1998 Yi Q, Bystroff C, Rajagopal P, Klevit RE, Baker D. Prediction and structural characterization of an independently folding substructure in the src SH3 domain. Journal of Molecular Biology. 283: 293-300. PMID 9761691 DOI: 10.1006/Jmbi.1998.2072  0.295
1998 Plaxco KW, Simons KT, Baker D. Contact order, transition state placement and the refolding rates of single domain proteins. Journal of Molecular Biology. 277: 985-94. PMID 9545386 DOI: 10.1006/Jmbi.1998.1645  0.294
1999 Scalley ML, Nauli S, Gladwin ST, Baker D. Structural transitions in the protein L denatured state ensemble. Biochemistry. 38: 15927-35. PMID 10625459 DOI: 10.1021/Bi991136G  0.294
2011 Bouvignies G, Vallurupalli P, Hansen DF, Correia BE, Lange O, Bah A, Vernon RM, Dahlquist FW, Baker D, Kay LE. Solution structure of a minor and transiently formed state of a T4 lysozyme mutant. Nature. 477: 111-4. PMID 21857680 DOI: 10.1038/Nature10349  0.294
2013 Giger L, Caner S, Obexer R, Kast P, Baker D, Ban N, Hilvert D. Evolution of a designed retro-aldolase leads to complete active site remodeling Nature Chemical Biology. 9: 494-498. PMID 23748672 DOI: 10.1038/Nchembio.1276  0.294
2007 Das R, Baker D. Automated de novo prediction of native-like RNA tertiary structures. Proceedings of the National Academy of Sciences of the United States of America. 104: 14664-9. PMID 17726102 DOI: 10.1073/Pnas.0703836104  0.294
2010 Ashworth J, Taylor GK, Havranek JJ, Quadri SA, Stoddard BL, Baker D. Computational reprogramming of homing endonuclease specificity at multiple adjacent base pairs. Nucleic Acids Research. 38: 5601-8. PMID 20435674 DOI: 10.1093/Nar/Gkq283  0.293
2011 Wu SJ, Eiben CB, Carra JH, Huang I, Zong D, Liu P, Wu CT, Nivala J, Dunbar J, Huber T, Senft J, Schokman R, Smith MD, Mills JH, Friedlander AM, Baker D, et al. Improvement of a potential anthrax therapeutic by computational protein design. The Journal of Biological Chemistry. 286: 32586-92. PMID 21768086 DOI: 10.1074/Jbc.M111.251041  0.293
2001 Grantcharova VP, Baker D. Circularization changes the folding transition state of the src SH3 domain. Journal of Molecular Biology. 306: 555-63. PMID 11178913 DOI: 10.1006/Jmbi.2000.4352  0.293
2001 Kuhlman B, O'Neill JW, Kim DE, Zhang KY, Baker D. 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. 98: 10687-91. PMID 11526208 DOI: 10.1073/Pnas.181354398  0.293
1996 Bystroff C, Simons KT, Han KF, Baker D. Local sequence-structure correlations in proteins. Current Opinion in Biotechnology. 7: 417-21. PMID 8768900 DOI: 10.1016/S0958-1669(96)80117-0  0.292
2004 Schlosshauer M, Baker D. Realistic protein-protein association rates from a simple diffusional model neglecting long-range interactions, free energy barriers, and landscape ruggedness. Protein Science : a Publication of the Protein Society. 13: 1660-9. PMID 15133165 DOI: 10.1110/Ps.03517304  0.292
2001 Bonneau R, Strauss CE, Baker D. Improving the performance of Rosetta using multiple sequence alignment information and global measures of hydrophobic core formation. Proteins. 43: 1-11. PMID 11170209 DOI: 10.1002/1097-0134(20010401)43:1<1::Aid-Prot1012>3.0.Co;2-A  0.291
2001 Hankey DJ, Lightman SL, Baker D. Interphotoreceptor retinoid binding protein peptide-induced uveitis in B10.RIII mice: characterization of disease parameters and immunomodulation. Experimental Eye Research. 72: 341-50. PMID 11180983 DOI: 10.1006/Exer.2000.0957  0.291
1998 Plaxco KW, Baker D. 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. 95: 13591-6. PMID 9811844 DOI: 10.1073/Pnas.95.23.13591  0.291
1999 Riddle DS, Grantcharova VP, Santiago JV, Alm E, Ruczinski I, Baker D. Experiment and theory highlight role of native state topology in SH3 folding. Nature Structural Biology. 6: 1016-24. PMID 10542092 DOI: 10.1038/14901  0.291
2014 Huang PS, Oberdorfer G, Xu C, Pei XY, Nannenga BL, Rogers JM, DiMaio F, Gonen T, Luisi B, Baker D. High thermodynamic stability of parametrically designed helical bundles. Science (New York, N.Y.). 346: 481-5. PMID 25342806 DOI: 10.1126/Science.1257481  0.291
1998 Gu H, Kim D, Baker D. Contrasting roles for symmetrically disposed beta-turns in the folding of a small protein. Journal of Molecular Biology. 274: 588-96. PMID 9417937 DOI: 10.1006/Jmbi.1997.1374  0.291
2012 King NP, Sheffler W, Sawaya MR, Vollmar BS, Sumida JP, André I, Gonen T, Yeates TO, Baker D. Computational design of self-assembling protein nanomaterials with atomic level accuracy. Science (New York, N.Y.). 336: 1171-4. PMID 22654060 DOI: 10.1126/Science.1219364  0.29
2015 Egelman EH, Xu C, DiMaio F, Magnotti E, Modlin C, Yu X, Wright E, Baker D, Conticello VP. Structural plasticity of helical nanotubes based on coiled-coil assemblies. Structure (London, England : 1993). 23: 280-9. PMID 25620001 DOI: 10.1016/J.Str.2014.12.008  0.29
2003 Scalley-Kim M, Minard P, Baker D. Low free energy cost of very long loop insertions in proteins. Protein Science : a Publication of the Protein Society. 12: 197-206. PMID 12538883 DOI: 10.1110/Ps.0232003  0.29
1993 Bystroff C, Baker D, Fletterick RJ, Agard DA. PRISM: application to the solution of two protein structures. Acta Crystallographica. Section D, Biological Crystallography. 49: 440-8. PMID 15299503 DOI: 10.1107/S0907444993004020  0.289
2011 Fleishman SJ, Whitehead TA, Ekiert DC, Dreyfus C, Corn JE, Strauch EM, Wilson IA, Baker D. Computational design of proteins targeting the conserved stem region of influenza hemagglutinin. Science (New York, N.Y.). 332: 816-21. PMID 21566186 DOI: 10.1126/Science.1202617  0.289
2009 Sadreyev RI, Shi S, Baker D, Grishin NV. Structure similarity measure with penalty for close non-equivalent residues. Bioinformatics (Oxford, England). 25: 1259-63. PMID 19321733 DOI: 10.1093/Bioinformatics/Btp148  0.289
1997 Scalley ML, Yi Q, Gu H, McCormack A, Yates JR, Baker D. Kinetics of folding of the IgG binding domain of peptostreptococcal protein L. Biochemistry. 36: 3373-82. PMID 9116017 DOI: 10.1021/Bi9625758  0.289
2007 Das R, Qian B, Raman S, Vernon R, Thompson J, Bradley P, Khare S, Tyka MD, Bhat D, Chivian D, Kim DE, Sheffler WH, Malmström L, Wollacott AM, Wang C, ... Baker D, et al. Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home. Proteins. 69: 118-28. PMID 17894356 DOI: 10.1002/Prot.21636  0.289
2019 Langan RA, Boyken SE, Ng AH, Samson JA, Dods G, Westbrook AM, Nguyen TH, Lajoie MJ, Chen Z, Berger S, Mulligan VK, Dueber JE, Novak WRP, El-Samad H, Baker D. De novo design of bioactive protein switches. Nature. PMID 31341284 DOI: 10.1038/S41586-019-1432-8  0.289
2006 Baker D. Prediction and design of macromolecular structures and interactions. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 361: 459-63. PMID 16524834 DOI: 10.1098/Rstb.2005.1803  0.288
1998 Grantcharova VP, Riddle DS, Santiago JV, Baker D. Important role of hydrogen bonds in the structurally polarized transition state for folding of the src SH3 domain. Nature Structural Biology. 5: 714-20. PMID 9699636 DOI: 10.1038/1412  0.288
2017 Van Pattten WJ, Walder R, Adhikari A, Ravichandran R, Tinberg CE, Baker D, Perkins TT. A Computationally Designed Protein-Ligand Interaction is Mechanically Robust Biophysical Journal. 112: 455a. DOI: 10.1016/J.Bpj.2016.11.2440  0.288
2008 Jiang L, Althoff EA, Clemente FR, Doyle L, Röthlisberger D, Zanghellini A, Gallaher JL, Betker JL, Tanaka F, Barbas CF, Hilvert D, Houk KN, Stoddard BL, Baker D. De novo computational design of retro-aldol enzymes. Science (New York, N.Y.). 319: 1387-91. PMID 18323453 DOI: 10.1126/Science.1152692  0.288
2012 Kellogg EH, Lange OF, Baker D. Evaluation and optimization of discrete state models of protein folding. The Journal of Physical Chemistry. B. 116: 11405-13. PMID 22958200 DOI: 10.1021/Jp3044303  0.288
2013 Adams PD, Baker D, Brunger AT, Das R, DiMaio F, Read RJ, Richardson DC, Richardson JS, Terwilliger TC. Advances, interactions, and future developments in the CNS, Phenix, and Rosetta structural biology software systems. Annual Review of Biophysics. 42: 265-87. PMID 23451892 DOI: 10.1146/Annurev-Biophys-083012-130253  0.287
2012 Tyka MD, Jung K, Baker D. Efficient sampling of protein conformational space using fast loop building and batch minimization on highly parallel computers. Journal of Computational Chemistry. 33: 2483-91. PMID 22847521 DOI: 10.1002/Jcc.23069  0.287
2018 Sahasrabuddhe A, Hsia Y, Busch F, Sheffler W, King NP, Baker D, Wysocki VH. 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. PMID 29351988 DOI: 10.1073/Pnas.1713646115  0.287
2016 Garcia KE, Babanova S, Scheffler W, Hans M, Baker D, Atanassov P, Banta S. Designed protein aggregates entrapping carbon nanotubes for bioelectrochemical oxygen reduction. Biotechnology and Bioengineering. PMID 27093643 DOI: 10.1002/Bit.25996  0.287
2017 Dang B, Wu H, Mulligan VK, Mravic M, Wu Y, Lemmin T, Ford A, Silva DA, Baker D, DeGrado WF. De novo design of covalently constrained mesosize protein scaffolds with unique tertiary structures. Proceedings of the National Academy of Sciences of the United States of America. PMID 28973862 DOI: 10.1073/Pnas.1710695114  0.286
1992 Baker D, Silen JL, Agard DA. Protease pro region required for folding is a potent inhibitor of the mature enzyme. Proteins. 12: 339-44. PMID 1579568 DOI: 10.1002/Prot.340120406  0.286
2008 Qiu J, Sheffler W, Baker D, Noble WS. Ranking predicted protein structures with support vector regression. Proteins. 71: 1175-82. PMID 18004754 DOI: 10.1002/Prot.21809  0.286
1997 Grantcharova VP, Baker D. Folding dynamics of the src SH3 domain. Biochemistry. 36: 15685-92. PMID 9398297 DOI: 10.1021/Bi971786P  0.285
2007 Goobes G, Goobes R, Shaw WJ, Gibson JM, Long JR, Raghunathan V, Schueler-Furman O, Popham JM, Baker D, Campbell CT, Stayton PS, Drobny GP. The structure, dynamics, and energetics of protein adsorption-lessons learned from adsorption of statherin to hydroxyapatite. Magnetic Resonance in Chemistry : Mrc. 45: S32-47. PMID 18172904 DOI: 10.1002/Mrc.2123  0.285
2009 Davis IW, Baker D. RosettaLigand docking with full ligand and receptor flexibility. Journal of Molecular Biology. 385: 381-92. PMID 19041878 DOI: 10.1016/J.Jmb.2008.11.010  0.284
2017 Yeh CT, Brunette TJ, Baker D, McIntosh-Smith S, Parmeggiani F. Elfin: an algorithm for the computational design of custom three-dimensional structures from modular repeat protein building blocks. Journal of Structural Biology. PMID 28890160 DOI: 10.1016/J.Jsb.2017.09.001  0.284
2001 Muhia DK, Swales CA, Deng W, Kelly JM, Baker DA. The gametocyte-activating factor xanthurenic acid stimulates an increase in membrane-associated guanylyl cyclase activity in the human malaria parasite Plasmodium falciparum. Molecular Microbiology. 42: 553-60. PMID 11703675 DOI: 10.1046/J.1365-2958.2001.02665.X  0.284
1997 Bystroff C, Baker D. Blind predictions of local protein structure in CASP2 targets using the I-sites library. Proteins. 167-71. PMID 9485508 DOI: 10.1002/(Sici)1097-0134(1997)1+<167::Aid-Prot21>3.0.Co;2-L  0.284
2012 Krzysiak TC, Jung J, Thompson J, Baker D, Gronenborn AM. APOBEC2 is a monomer in solution: Implications for APOBEC3G Models Biochemistry. 51: 2008-2017. PMID 22339232 DOI: 10.1021/Bi300021S  0.284
2015 Kudryashev M, Wang RY, Brackmann M, Scherer S, Maier T, Baker D, DiMaio F, Stahlberg H, Egelman EH, Basler M. Structure of the type VI secretion system contractile sheath. Cell. 160: 952-62. PMID 25723169 DOI: 10.1016/J.Cell.2015.01.037  0.284
2012 Wang L, Althoff EA, Bolduc J, Jiang L, Moody J, Lassila JK, Giger L, Hilvert D, Stoddard B, Baker D. Structural analyses of covalent enzyme-substrate analog complexes reveal strengths and limitations of de novo enzyme design. Journal of Molecular Biology. 415: 615-25. PMID 22075445 DOI: 10.1016/J.Jmb.2011.10.043  0.284
2018 Silva DA, Stewart L, Lam KH, Jin R, Baker D. Structures and disulfide cross-linking of de novo designed therapeutic mini-proteins. The Febs Journal. PMID 29389072 DOI: 10.1111/Febs.14394  0.284
2012 Eiben CB, Siegel JB, Bale JB, Cooper S, Khatib F, Shen BW, Players F, Stoddard BL, Popovic Z, Baker D. Increased Diels-Alderase activity through backbone remodeling guided by Foldit players. Nature Biotechnology. 30: 190-2. PMID 22267011 DOI: 10.1038/Nbt.2109  0.284
2017 Chevalier A, Silva DA, Rocklin GJ, Hicks DR, Vergara R, Murapa P, Bernard SM, Zhang L, Lam KH, Yao G, Bahl CD, Miyashita SI, Goreshnik I, Fuller JT, Koday MT, ... ... Baker D, et al. Massively parallel de novo protein design for targeted therapeutics. Nature. PMID 28953867 DOI: 10.1038/Nature23912  0.284
2011 Valkov E, Stamp A, Dimaio F, Baker D, Verstak B, Roversi P, Kellie S, Sweet MJ, Mansell A, Gay NJ, Martin JL, Kobe B. 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. 108: 14879-84. PMID 21873236 DOI: 10.1073/Pnas.1104780108  0.284
2014 Procko E, Berguig GY, Shen BW, Song Y, Frayo S, Convertine AJ, Margineantu D, Booth G, Correia BE, Cheng Y, Schief WR, Hockenbery DM, Press OW, Stoddard BL, Stayton PS, Baker D, et al. A computationally designed inhibitor of an Epstein-Barr viral Bcl-2 protein induces apoptosis in infected cells. Cell. 157: 1644-56. PMID 24949974 DOI: 10.1016/J.Cell.2014.04.034  0.283
1999 Plaxco KW, Millett IS, Segel DJ, Doniach S, Baker D. Chain collapse can occur concomitantly with the rate-limiting step in protein folding. Nature Structural Biology. 6: 554-6. PMID 10360359 DOI: 10.1038/9329  0.283
1993 Baker D, Shiau AK, Agard DA. The role of pro regions in protein folding. Current Opinion in Cell Biology. 5: 966-70. PMID 8129949 DOI: 10.1016/0955-0674(93)90078-5  0.283
2005 Kim DE, Chivian D, Malmström L, Baker D. Automated prediction of domain boundaries in CASP6 targets using Ginzu and RosettaDOM. Proteins. 61: 193-200. PMID 16187362 DOI: 10.1002/Prot.20737  0.283
2000 Thoua NM, van Noort JM, Baker D, Bose A, van Sechel AC, van Stipdonk MJ, Travers PJ, Amor S. Encephalitogenic and immunogenic potential of the stress protein alphaB-crystallin in Biozzi ABH (H-2A(g7)) mice. Journal of Neuroimmunology. 104: 47-57. PMID 10683514 DOI: 10.1016/S0165-5728(99)00246-5  0.283
2011 Song Y, Tyka M, Leaver-Fay A, Thompson J, Baker D. Structure-guided forcefield optimization. Proteins. 79: 1898-909. PMID 21488100 DOI: 10.1002/Prot.23013  0.283
2000 Grantcharova VP, Riddle DS, Baker D. Long-range order in the src SH3 folding transition state. Proceedings of the National Academy of Sciences of the United States of America. 97: 7084-9. PMID 10860975 DOI: 10.1073/Pnas.97.13.7084  0.283
2016 Hurley MM, Maunze B, Block ME, Frenkel MM, Reilly MJ, Kim E, Chen Y, Li Y, Baker DA, Liu QS, Choi S. Pituitary Adenylate-Cyclase Activating Polypeptide Regulates Hunger- and Palatability-Induced Binge Eating. Frontiers in Neuroscience. 10: 383. PMID 27597817 DOI: 10.3389/Fnins.2016.00383  0.283
2004 Chen Y, Kortemme T, Robertson T, Baker D, Varani G. A new hydrogen-bonding potential for the design of protein-RNA interactions predicts specific contacts and discriminates decoys. Nucleic Acids Research. 32: 5147-62. PMID 15459285 DOI: 10.1093/Nar/Gkh785  0.283
2019 Koepnick B, Flatten J, Husain T, Ford A, Silva DA, Bick MJ, Bauer A, Liu G, Ishida Y, Boykov A, Estep RD, Kleinfelter S, Nørgård-Solano T, Wei L, Players F, ... ... Baker D, et al. De novo protein design by citizen scientists. Nature. PMID 31168091 DOI: 10.1038/S41586-019-1274-4  0.283
2013 Moretti R, Fleishman SJ, Agius R, Torchala M, Bates PA, Kastritis PL, Rodrigues JP, Trellet M, Bonvin AM, Cui M, Rooman M, Gillis D, Dehouck Y, Moal I, Romero-Durana M, ... Baker D, et al. Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions. Proteins. 81: 1980-7. PMID 23843247 DOI: 10.1002/Prot.24356  0.283
2020 Basanta B, Bick MJ, Bera AK, Norn C, Chow CM, Carter LP, Goreshnik I, Dimaio F, Baker D. An enumerative algorithm for de novo design of proteins with diverse pocket structures. Proceedings of the National Academy of Sciences of the United States of America. PMID 32839327 DOI: 10.1073/Pnas.2005412117  0.283
2012 Schmitz C, Vernon R, Otting G, Baker D, Huber T. Protein structure determination from pseudocontact shifts using ROSETTA. Journal of Molecular Biology. 416: 668-77. PMID 22285518 DOI: 10.1016/J.Jmb.2011.12.056  0.283
2013 Whitehead TA, Baker D, Fleishman SJ. Computational design of novel protein binders and experimental affinity maturation. Methods in Enzymology. 523: 1-19. PMID 23422423 DOI: 10.1016/B978-0-12-394292-0.00001-1  0.283
2000 Kim DE, Fisher C, Baker D. A breakdown of symmetry in the folding transition state of protein L. Journal of Molecular Biology. 298: 971-84. PMID 10801362 DOI: 10.1006/Jmbi.2000.3701  0.283
2000 Yi Q, Scalley-Kim ML, Alm EJ, Baker D. NMR characterization of residual structure in the denatured state of protein L. Journal of Molecular Biology. 299: 1341-51. PMID 10873457 DOI: 10.1006/Jmbi.2000.3816  0.282
1999 Gu H, Doshi N, Kim DE, Simons KT, Santiago JV, Nauli S, Baker D. Robustness of protein folding kinetics to surface hydrophobic substitutions. Protein Science : a Publication of the Protein Society. 8: 2734-41. PMID 10631990 DOI: 10.1110/Ps.8.12.2734  0.282
2003 Wedemeyer WJ, Baker D. Efficient minimization of angle-dependent potentials for polypeptides in internal coordinates. Proteins. 53: 262-72. PMID 14517977 DOI: 10.1002/Prot.10525  0.282
2006 Goobes G, Goobes R, Schueler-Furman O, Baker D, Stayton PS, Drobny GP. 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. 103: 16083-8. PMID 17060618 DOI: 10.1073/Pnas.0607193103  0.282
2016 Boyken SE, Chen Z, Groves B, Langan RA, Oberdorfer G, Ford A, Gilmore JM, Xu C, DiMaio F, Pereira JH, Sankaran B, Seelig G, Zwart PH, Baker D. De novo design of protein homo-oligomers with modular hydrogen-bond network-mediated specificity. Science (New York, N.Y.). 352: 680-7. PMID 27151862 DOI: 10.1126/Science.Aad8865  0.282
2016 Crook ZR, Bradley P, King C, Mhyre AJ, Baker D, Olson JM. Abstract 2971: Optides (optimized knottin peptides) computationally designed to target the oncogenic HIPPO pathway Cancer Research. 76: 2971-2971. DOI: 10.1158/1538-7445.Am2016-2971  0.281
2002 Krantz BA, Srivastava AK, Nauli S, Baker D, Sauer RT, Sosnick TR. Understanding protein hydrogen bond formation with kinetic H/D amide isotope effects. Nature Structural Biology. 9: 458-63. PMID 11979278 DOI: 10.1038/Nsb794  0.281
2016 Huang PS, Boyken SE, Baker D. The coming of age of de novo protein design. Nature. 537: 320-327. PMID 27629638 DOI: 10.1038/Nature19946  0.281
2020 Wei KY, Moschidi D, Bick MJ, Nerli S, McShan AC, Carter LP, Huang PS, Fletcher DA, Sgourakis NG, Boyken SE, Baker D. Computational design of closely related proteins that adopt two well-defined but structurally divergent folds. Proceedings of the National Academy of Sciences of the United States of America. PMID 32188784 DOI: 10.1073/Pnas.1914808117  0.281
1997 Yi Q, Scalley ML, Simons KT, Gladwin ST, Baker D. Characterization of the free energy spectrum of peptostreptococcal protein L. Folding & Design. 2: 271-80. PMID 9377710 DOI: 10.1016/S1359-0278(97)00038-2  0.281
2013 Mills JH, Khare SD, Bolduc JM, Forouhar F, Mulligan VK, Lew S, Seetharaman J, Tong L, Stoddard BL, Baker D. Computational design of an unnatural amino acid dependent metalloprotein with atomic level accuracy. Journal of the American Chemical Society. 135: 13393-9. PMID 23924187 DOI: 10.1021/Ja403503M  0.281
2005 Chivian D, Kim DE, Malmström L, Schonbrun J, Rohl CA, Baker D. Prediction of CASP6 structures using automated Robetta protocols. Proteins. 61: 157-66. PMID 16187358 DOI: 10.1002/Prot.20733  0.28
2019 Park J, Selvaraj B, McShan AC, Boyken SE, Wei KY, Oberdorfer G, DeGrado W, Sgourakis NG, Cuneo MJ, Myles DA, Baker D. De novo design of a homo-trimeric amantadine-binding protein. Elife. 8. PMID 31854299 DOI: 10.7554/Elife.47839  0.28
2017 Rocklin GJ, Chidyausiku T, Goreshnik I, Ford A, Houliston S, Arrowsmith C, Baker D. High-Throughput Protein Design Reveals Quantitative Protein Stability Requirements Biophysical Journal. 112: 194a. DOI: 10.1016/J.Bpj.2016.11.1076  0.28
2000 Croxford JL, Triantaphyllopoulos KA, Neve RM, Feldmann M, Chernajovsky Y, Baker D. Gene therapy for chronic relapsing experimental allergic encephalomyelitis using cells expressing a novel soluble p75 dimeric TNF receptor. Journal of Immunology. 164: 2776-2781. PMID 10679120 DOI: 10.4049/Jimmunol.164.5.2776  0.28
2014 Preiswerk N, Beck T, Schulz JD, Milovník P, Mayer C, Siegel JB, Baker D, Hilvert D. 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. 111: 8013-8. PMID 24847076 DOI: 10.1073/Pnas.1401073111  0.28
2010 Sampathkumar P, Lu F, Zhao X, Li Z, Gilmore J, Bain K, Rutter ME, Gheyi T, Schwinn KD, Bonanno JB, Pieper U, Fajardo JE, Fiser A, Almo SC, Swaminathan S, ... ... Baker D, et al. Structure of a putative BenF-like porin from Pseudomonas fluorescens Pf-5 at 2.6 A resolution. Proteins. 78: 3056-62. PMID 20737437 DOI: 10.1002/Prot.22829  0.28
2010 Fleishman SJ, Corn JE, Strauch EM, Whitehead TA, Andre I, Thompson J, Havranek JJ, Das R, Bradley P, Baker D. Rosetta in CAPRI rounds 13-19. Proteins. 78: 3212-8. PMID 20597089 DOI: 10.1002/Prot.22784  0.28
2010 Kiss G, Röthlisberger D, Baker D, Houk KN. Evaluation and ranking of enzyme designs. Protein Science : a Publication of the Protein Society. 19: 1760-73. PMID 20665693 DOI: 10.1002/Pro.462  0.28
2009 Ramelot TA, Raman S, Kuzin AP, Xiao R, Ma LC, Acton TB, Hunt JF, Montelione GT, Baker D, Kennedy MA. Improving NMR protein structure quality by Rosetta refinement: a molecular replacement study. Proteins. 75: 147-67. PMID 18816799 DOI: 10.1002/Prot.22229  0.28
1997 Han KF, Bystroff C, Baker D. Three-dimensional structures and contexts associated with recurrent amino acid sequence patterns. Protein Science : a Publication of the Protein Society. 6: 1587-90. PMID 9232660 DOI: 10.1002/Pro.5560060723  0.28
2020 Brunette TJ, Bick MJ, Hansen JM, Chow CM, Kollman JM, Baker D. Modular repeat protein sculpting using rigid helical junctions. Proceedings of the National Academy of Sciences of the United States of America. PMID 32245816 DOI: 10.1073/Pnas.1908768117  0.28
2004 Morozov AY, Misura KMS, Tsemekhman K, Baker D. Comparison of quantum mechanics and molecular mechanics dimerization energy landscapes for pairs of ring-containing amino acids in proteins Journal of Physical Chemistry B. 108: 8489-8496. DOI: 10.1021/Jp037711E  0.279
2015 Wang RY, Kudryashev M, Li X, Egelman EH, Basler M, Cheng Y, Baker D, DiMaio F. De novo protein structure determination from near-atomic-resolution cryo-EM maps. Nature Methods. 12: 335-8. PMID 25707029 DOI: 10.1038/Nmeth.3287  0.279
2004 Kuhn M, Meiler J, Baker D. Strand-loop-strand motifs: prediction of hairpins and diverging turns in proteins. Proteins. 54: 282-8. PMID 14696190 DOI: 10.1002/Prot.10589  0.279
2019 Pyles H, Zhang S, De Yoreo JJ, Baker D. Controlling protein assembly on inorganic crystals through designed protein interfaces. Nature. 571: 251-256. PMID 31292559 DOI: 10.1038/S41586-019-1361-6  0.279
2004 Qian B, Ortiz AR, Baker D. 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. 101: 15346-51. PMID 15492216 DOI: 10.1073/Pnas.0404703101  0.279
2015 Bergeron JR, Worrall LJ, De S, Sgourakis NG, Cheung AH, Lameignere E, Okon M, Wasney GA, Baker D, McIntosh LP, Strynadka NC. The modular structure of the inner-membrane ring component PrgK facilitates assembly of the type III secretion system basal body. Structure (London, England : 1993). 23: 161-72. PMID 25533490 DOI: 10.1016/J.Str.2014.10.021  0.279
1995 Han KF, Baker D. Recurring local sequence motifs in proteins. Journal of Molecular Biology. 251: 176-87. PMID 7643386 DOI: 10.1006/Jmbi.1995.0424  0.279
2014 Obexer R, Studer S, Giger L, Pinkas DM, Grütter MG, Baker D, Hilvert D. Active site plasticity of a computationally designed retro-aldolase enzyme Chemcatchem. 6: 1043-1050. DOI: 10.1002/Cctc.201300933  0.279
2002 Saunders CT, Baker D. Evaluation of structural and evolutionary contributions to deleterious mutation prediction. Journal of Molecular Biology. 322: 891-901. PMID 12270722 DOI: 10.1016/S0022-2836(02)00813-6  0.278
2011 Sievers SA, Karanicolas J, Chang HW, Zhao A, Jiang L, Zirafi O, Stevens JT, Münch J, Baker D, Eisenberg D. Structure-based design of non-natural amino-acid inhibitors of amyloid fibril formation. Nature. 475: 96-100. PMID 21677644 DOI: 10.1038/Nature10154  0.278
2020 Chen Z, Kibler RD, Hunt A, Busch F, Pearl J, Jia M, VanAernum ZL, Wicky BIM, Dods G, Liao H, Wilken MS, Ciarlo C, Green S, El-Samad H, Stamatoyannopoulos J, ... ... Baker D, et al. De novo design of protein logic gates. Science (New York, N.Y.). 368: 78-84. PMID 32241946 DOI: 10.1126/Science.Aay2790  0.278
2007 Stankunas K, Bayle JH, Havranek JJ, Wandless TJ, Baker D, Crabtree GR, Gestwicki JE. Rescue of degradation-prone mutants of the FK506-rapamycin binding (FRB) protein with chemical ligands. Chembiochem : a European Journal of Chemical Biology. 8: 1162-9. PMID 17525916 DOI: 10.1002/Cbic.200700087  0.278
2009 Thyme SB, Jarjour J, Takeuchi R, Havranek JJ, Ashworth J, Scharenberg AM, Stoddard BL, Baker D. Exploitation of binding energy for catalysis and design. Nature. 461: 1300-4. PMID 19865174 DOI: 10.1038/Nature08508  0.278
2015 King IC, Gleixner J, Doyle L, Kuzin A, Hunt JF, Xiao R, Montelione GT, Stoddard BL, DiMaio F, Baker D. Precise assembly of complex beta sheet topologies from de novo designed building blocks. Elife. 4. PMID 26650357 DOI: 10.7554/Elife.11012  0.278
2001 Bonneau R, Baker D. Ab initio protein structure prediction: progress and prospects. Annual Review of Biophysics and Biomolecular Structure. 30: 173-89. PMID 11340057 DOI: 10.1146/Annurev.Biophys.30.1.173  0.278
2016 Basanta B, Chan KK, Barth P, King T, Hinshaw JR, Sosnick TR, Liu G, Everett J, Xiao R, Montelione GT, Baker D. Introduction of a polar core into the de novo designed protein Top7. Protein Science : a Publication of the Protein Society. PMID 26873166 DOI: 10.1002/Pro.2899  0.278
2017 Moody JD, Levy S, Mathieu J, Xing Y, Kim W, Dong C, Tempel W, Robitaille AM, Dang LT, Ferreccio A, Detraux D, Sidhu S, Zhu L, Carter L, Xu C, ... ... Baker D, et al. First critical repressive H3K27me3 marks in embryonic stem cells identified using designed protein inhibitor. Proceedings of the National Academy of Sciences of the United States of America. PMID 28864533 DOI: 10.1073/Pnas.1706907114  0.277
2017 Rocklin GJ, Chidyausiku TM, Goreshnik I, Ford A, Houliston S, Lemak A, Carter L, Ravichandran R, Mulligan VK, Chevalier A, Arrowsmith CH, Baker D. Global analysis of protein folding using massively parallel design, synthesis, and testing. Science (New York, N.Y.). 357: 168-175. PMID 28706065 DOI: 10.1126/Science.Aan0693  0.277
2016 Rödström KE, Regenthal P, Bahl C, Ford A, Baker D, Lindkvist-Petersson K. Two common structural motifs for TCR recognition by staphylococcal enterotoxins. Scientific Reports. 6: 25796. PMID 27180909 DOI: 10.1038/Srep25796  0.277
2012 Gordon SR, Stanley EJ, Wolf S, Toland A, Wu SJ, Hadidi D, Mills JH, Baker D, Pultz IS, Siegel JB. Computational design of an α-gliadin peptidase. Journal of the American Chemical Society. 134: 20513-20. PMID 23153249 DOI: 10.1021/Ja3094795  0.277
2018 Geiger-Schuller K, Sforza K, Yuhas M, Parmeggiani F, Baker D, Barrick D. 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. PMID 29959204 DOI: 10.1073/Pnas.1800283115  0.277
2008 André I, Strauss CE, Kaplan DB, Bradley P, Baker D. Emergence of symmetry in homooligomeric biological assemblies. Proceedings of the National Academy of Sciences of the United States of America. 105: 16148-52. PMID 18849473 DOI: 10.1073/Pnas.0807576105  0.277
2006 Thompson MJ, Sievers SA, Karanicolas J, Ivanova MI, Baker D, Eisenberg D. The 3D profile method for identifying fibril-forming segments of proteins. Proceedings of the National Academy of Sciences of the United States of America. 103: 4074-8. PMID 16537487 DOI: 10.1073/Pnas.0511295103  0.277
2010 Leung CC, Kellogg E, Kuhnert A, Hänel F, Baker D, Glover JN. Insights from the crystal structure of the sixth BRCT domain of topoisomerase IIbeta binding protein 1. Protein Science : a Publication of the Protein Society. 19: 162-7. PMID 19937654 DOI: 10.1002/Pro.290  0.277
2010 Khersonsky O, Röthlisberger D, Dym O, Albeck S, Jackson CJ, Baker D, Tawfik DS. Evolutionary optimization of computationally designed enzymes: Kemp eliminases of the KE07 series. Journal of Molecular Biology. 396: 1025-42. PMID 20036254 DOI: 10.1016/J.Jmb.2009.12.031  0.277
2014 Strauch EM, Fleishman SJ, Baker D. Computational design of a pH-sensitive IgG binding protein. Proceedings of the National Academy of Sciences of the United States of America. 111: 675-80. PMID 24381156 DOI: 10.1073/Pnas.1313605111  0.276
2005 Jackson SJ, Baker D, Cuzner ML, Diemel LT. Cannabinoid-mediated neuroprotection following interferon-gamma treatment in a three-dimensional mouse brain aggregate cell culture. The European Journal of Neuroscience. 20: 2267-75. PMID 15525268 DOI: 10.1111/J.1460-9568.2004.03711.X  0.276
1988 Payne GS, Baker D, Van Tuinen E, Schekman R. Protein transport to the vacuole and receptor-mediated endocytosis by clathrin heavy chain-deficient yeast Journal of Cell Biology. 106: 1453-1461. PMID 2836429 DOI: 10.1083/Jcb.106.5.1453  0.276
2007 Lengyel CS, Willis LJ, Mann P, Baker D, Kortemme T, Strong RK, McFarland BJ. Mutations designed to destabilize the receptor-bound conformation increase MICA-NKG2D association rate and affinity. The Journal of Biological Chemistry. 282: 30658-66. PMID 17690100 DOI: 10.1074/Jbc.M704513200  0.276
2003 Yi Q, Rajagopal P, Klevit RE, Baker D. Structural and kinetic characterization of the simplified SH3 domain FP1 Protein Science. 12: 776-783. PMID 12649436 DOI: 10.1110/Ps.0238603  0.276
2006 Sood VD, Baker D. Recapitulation and design of protein binding peptide structures and sequences. Journal of Molecular Biology. 357: 917-27. PMID 16473368 DOI: 10.1016/J.Jmb.2006.01.045  0.276
1994 Baker D, Butler D, Scallon BJ, O'Neill JK, Turk JL, Feldmann M. 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. 24: 2040-2048. PMID 8088324 DOI: 10.1002/Eji.1830240916  0.275
2008 Sawaya MR, Wojtowicz WM, Andre I, Qian B, Wu W, Baker D, Eisenberg D, Zipursky SL. A double S shape provides the structural basis for the extraordinary binding specificity of Dscam isoforms. Cell. 134: 1007-18. PMID 18805093 DOI: 10.1016/J.Cell.2008.07.042  0.275
2014 Wijma HJ, Floor RJ, Jekel PA, Baker D, Marrink SJ, Janssen DB. Computationally designed libraries for rapid enzyme stabilization Protein Engineering, Design and Selection. 27: 49-58. PMID 24402331 DOI: 10.1093/Protein/Gzt061  0.275
2001 Lee MR, Baker D, Kollman PA. 2.1 and 1.8 A average C(alpha) RMSD structure predictions on two small proteins, HP-36 and s15. Journal of the American Chemical Society. 123: 1040-6. PMID 11456657 DOI: 10.1021/Ja003150I  0.275
2009 Davis IW, Raha K, Head MS, Baker D. Blind docking of pharmaceutically relevant compounds using RosettaLigand. Protein Science : a Publication of the Protein Society. 18: 1998-2002. PMID 19554568 DOI: 10.1002/Pro.192  0.275
2019 Ng AH, Nguyen TH, Gómez-Schiavon M, Dods G, Langan RA, Boyken SE, Samson JA, Waldburger LM, Dueber JE, Baker D, El-Samad H. Modular and tunable biological feedback control using a de novo protein switch. Nature. PMID 31341280 DOI: 10.1038/S41586-019-1425-7  0.275
2015 Ramaglia V, Jackson SJ, Hughes TR, Neal JW, Baker D, Morgan BP. Complement activation and expression during chronic relapsing experimental autoimmune encephalomyelitis in the Biozzi ABH mouse. Clinical and Experimental Immunology. 180: 432-41. PMID 25619542 DOI: 10.1111/Cei.12595  0.275
2015 Ramdani G, Naissant B, Thompson E, Breil F, Lorthiois A, Dupuy F, Cummings R, Duffier Y, Corbett Y, Mercereau-Puijalon O, Vernick K, Taramelli D, Baker DA, Langsley G, Lavazec C. cAMP-Signalling Regulates Gametocyte-Infected Erythrocyte Deformability Required for Malaria Parasite Transmission. Plos Pathogens. 11: e1004815. PMID 25951195 DOI: 10.1371/Journal.Ppat.1004815  0.275
2005 Jackson SJ, Pryce G, Diemel LT, Cuzner ML, Baker D. Cannabinoid-receptor 1 null mice are susceptible to neurofilament damage and caspase 3 activation. Neuroscience. 134: 261-268. PMID 15953683 DOI: 10.1016/J.Neuroscience.2005.02.045  0.275
2019 Flueck C, Drought LG, Jones A, Patel A, Perrin AJ, Walker EM, Nofal SD, Snijders AP, Blackman MJ, Baker DA. Phosphodiesterase beta is the master regulator of cAMP signalling during malaria parasite invasion. Plos Biology. 17: e3000154. PMID 30794532 DOI: 10.1371/Journal.Pbio.3000154  0.274
2006 Song G, Lazar GA, Kortemme T, Shimaoka M, Desjarlais JR, Baker D, Springer TA. Rational design of intercellular adhesion molecule-1 (ICAM-1) variants for antagonizing integrin lymphocyte function-associated antigen-1-dependent adhesion. The Journal of Biological Chemistry. 281: 5042-9. PMID 16354667 DOI: 10.1074/Jbc.M510454200  0.274
2013 Delarasse C, Smith P, Baker D, Amor S. Novel pathogenic epitopes of myelin oligodendrocyte glycoprotein induce experimental autoimmune encephalomyelitis in C57BL/6 mice Immunology. 140: 456-464. PMID 23876060 DOI: 10.1111/Imm.12155  0.274
2017 Crook ZR, Bradley P, Sevilla G, Friend D, King C, Mhyre A, Strong R, Baker D, Olson JM. Abstract 5573: A high-affinity Optide (optimized peptide) inhibitor of the Hippo pathway’s YAP-TEAD interaction Cancer Research. 77: 5573-5573. DOI: 10.1158/1538-7445.Am2017-5573  0.274
2012 Azoitei ML, Ban YE, Julien JP, Bryson S, Schroeter A, Kalyuzhniy O, Porter JR, Adachi Y, Baker D, Pai EF, Schief WR. Computational design of high-affinity epitope scaffolds by backbone grafting of a linear epitope. Journal of Molecular Biology. 415: 175-92. PMID 22061265 DOI: 10.1016/J.Jmb.2011.10.003  0.274
2015 Morag O, Sgourakis NG, Baker D, Goldbourt A. 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. 112: 971-6. PMID 25587134 DOI: 10.1073/Pnas.1415393112  0.274
2006 Bradley P, Baker D. Improved beta-protein structure prediction by multilevel optimization of nonlocal strand pairings and local backbone conformation. Proteins. 65: 922-9. PMID 17034045 DOI: 10.1002/Prot.21133  0.274
2011 Zhang J, Ma B, DiMaio F, Douglas NR, Joachimiak LA, Baker D, Frydman J, Levitt M, Chiu W. Cryo-EM structure of a group II chaperonin in the prehydrolysis ATP-bound state leading to lid closure. Structure (London, England : 1993). 19: 633-9. PMID 21565698 DOI: 10.1016/J.Str.2011.03.005  0.274
2010 Sanowar S, Singh P, Pfuetzner RA, André I, Zheng H, Spreter T, Strynadka NC, Gonen T, Baker D, Goodlett DR, Miller SI. Interactions of the transmembrane polymeric rings of the Salmonella enterica serovar Typhimurium type III secretion system. Mbio. 1. PMID 20824104 DOI: 10.1128/Mbio.00158-10  0.273
2014 Bjelic S, Kipnis Y, Wang L, Pianowski Z, Vorobiev S, Su M, Seetharaman J, Xiao R, Kornhaber G, Hunt JF, Tong L, Hilvert D, Baker D. Exploration of alternate catalytic mechanisms and optimization strategies for retroaldolase design. Journal of Molecular Biology. 426: 256-71. PMID 24161950 DOI: 10.1016/J.Jmb.2013.10.012  0.273
2018 Shen H, Fallas JA, Lynch E, Sheffler W, Parry B, Jannetty N, Decarreau J, Wagenbach M, Vicente JJ, Chen J, Wang L, Dowling Q, Oberdorfer G, Stewart L, Wordeman L, ... ... Baker D, et al. De novo design of self-assembling helical protein filaments. Science (New York, N.Y.). 362: 705-709. PMID 30409885 DOI: 10.2210/Pdb6E9R/Pdb  0.273
2015 Vittal V, Shi L, Wenzel DM, Scaglione KM, Duncan ED, Basrur V, Elenitoba-Johnson KS, Baker D, Paulson HL, Brzovic PS, Klevit RE. Intrinsic disorder drives N-terminal ubiquitination by Ube2w. Nature Chemical Biology. 11: 83-9. PMID 25436519 DOI: 10.1038/Nchembio.1700  0.273
2012 Baxter S, Lambert AR, Kuhar R, Jarjour J, Kulshina N, Parmeggiani F, Danaher P, Gano J, Baker D, Stoddard BL, Scharenberg AM. Engineering domain fusion chimeras from I-OnuI family LAGLIDADG homing endonucleases. Nucleic Acids Research. 40: 7985-8000. PMID 22684507 DOI: 10.1093/Nar/Gks502  0.273
2010 Cooper S, Khatib F, Treuille A, Barbero J, Lee J, Beenen M, Leaver-Fay A, Baker D, Popovi? Z, Players F. Predicting protein structures with a multiplayer online game. Nature. 466: 756-60. PMID 20686574 DOI: 10.1038/Nature09304  0.273
1992 O'Neill JK, Baker D, Davison AN, Maggon KK, Jaffee BD, Turk JL. 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. 38: 53-62. PMID 1577953 DOI: 10.1016/0165-5728(92)90090-8  0.273
2000 Johnsen K, O'Neill JW, Kim DE, Baker D, Zhang KY. Crystallization and preliminary X-ray diffraction studies of mutants of B1 IgG-binding domain of protein L from Peptostreptococcus magnus. Acta Crystallographica. Section D, Biological Crystallography. 56: 506-8. PMID 10739935 DOI: 10.1107/S0907444900002195  0.272
2013 Wittenberg G, Sheffler W, Darchi D, Baker D, Noy D. Accelerated electron transport from photosystem I to redox partners by covalently linked ferredoxin. Physical Chemistry Chemical Physics : Pccp. 15: 19608-14. PMID 24129892 DOI: 10.1039/C3Cp53264J  0.272
2006 Cabranes A, Pryce G, Baker D, Fernández-Ruiz J. Changes in CB1 receptors in motor-related brain structures of chronic relapsing experimental allergic encephalomyelitis mice. Brain Research. 1107: 199-205. PMID 16822488 DOI: 10.1016/J.Brainres.2006.06.001  0.272
2013 Bjelic S, Nivón LG, Çelebi-Ölçüm N, Kiss G, Rosewall CF, Lovick HM, Ingalls EL, Gallaher JL, Seetharaman J, Lew S, Montelione GT, Hunt JF, Michael FE, Houk KN, Baker D. Computational design of enone-binding proteins with catalytic activity for the Morita-Baylis-Hillman reaction. Acs Chemical Biology. 8: 749-57. PMID 23330600 DOI: 10.1021/Cb3006227  0.272
2008 Cho HD, Sood VD, Baker D, Weiner AM. On the role of a conserved, potentially helix-breaking residue in the tRNA-binding alpha-helix of archaeal CCA-adding enzymes. Rna (New York, N.Y.). 14: 1284-9. PMID 18495940 DOI: 10.1261/Rna.1060308  0.272
2015 Alam MM, Solyakov L, Bottrill AR, Flueck C, Siddiqui FA, Singh S, Mistry S, Viskaduraki M, Lee K, Hopp CS, Chitnis CE, Doerig C, Moon RW, Green JL, Holder AA, ... Baker DA, et al. Phosphoproteomics reveals malaria parasite Protein Kinase G as a signalling hub regulating egress and invasion. Nature Communications. 6: 7285. PMID 26149123 DOI: 10.1038/Ncomms8285  0.272
2009 Muratore KE, Seeliger MA, Wang Z, Fomina D, Neiswinger J, Havranek JJ, Baker D, Kuriyan J, Cole PA. Comparative analysis of mutant tyrosine kinase chemical rescue. Biochemistry. 48: 3378-86. PMID 19260709 DOI: 10.1021/Bi900057G  0.272
2014 Alushin GM, Lander GC, Kellogg EH, Zhang R, Baker D, Nogales E. High-resolution microtubule structures reveal the structural transitions in αβ-tubulin upon GTP hydrolysis. Cell. 157: 1117-29. PMID 24855948 DOI: 10.1016/J.Cell.2014.03.053  0.272
2014 Thyme SB, Song Y, Brunette TJ, Szeto MD, Kusak L, Bradley P, Baker D. Massively parallel determination and modeling of endonuclease substrate specificity. Nucleic Acids Research. 42: 13839-52. PMID 25389263 DOI: 10.1093/Nar/Gku1096  0.272
2013 Lidster K, Jackson SJ, Ahmed Z, Munro P, Coffey P, Giovannoni G, Baker MD, Baker D. Neuroprotection in a novel mouse model of multiple sclerosis. Plos One. 8: e79188. PMID 24223903 DOI: 10.1371/Journal.Pone.0079188  0.272
2013 Song Y, DiMaio F, Wang RY, Kim D, Miles C, Brunette T, Thompson J, Baker D. High-resolution comparative modeling with RosettaCM. Structure (London, England : 1993). 21: 1735-42. PMID 24035711 DOI: 10.1016/J.Str.2013.08.005  0.272
2006 Sprague ER, Wang C, Baker D, Bjorkman PJ. Crystal structure of the HSV-1 Fc receptor bound to Fc reveals a mechanism for antibody bipolar bridging. Plos Biology. 4: e148. PMID 16646632 DOI: 10.1371/Journal.Pbio.0040148  0.271
2013 Kipnis Y, Baker D. Comparison of designed and randomly generated catalysts for simple chemical reactions. Protein Science : a Publication of the Protein Society. 21: 1388-95. PMID 22811380 DOI: 10.1002/Pro.2125  0.271
2019 Chen Z, Boyken SE, Jia M, Busch F, Flores-Solis D, Bick MJ, Lu P, VanAernum ZL, Sahasrabuddhe A, Langan RA, Bermeo S, Brunette TJ, Mulligan VK, Carter LP, DiMaio F, ... ... Baker D, et al. Programmable design of orthogonal protein heterodimers. Nature. 565: 106-111. PMID 30568301 DOI: 10.1038/s41586-018-0802-y  0.271
2016 Hurley MM, Resch JM, Maunze B, Frenkel MM, Baker DA, Choi S. N-acetylcysteine decreases binge eating in a rodent model. International Journal of Obesity (2005). PMID 26975440 DOI: 10.1038/Ijo.2016.31  0.271
2009 Luo BH, Karanicolas J, Harmacek LD, Baker D, Springer TA. Rationally designed integrin beta3 mutants stabilized in the high affinity conformation. The Journal of Biological Chemistry. 284: 3917-24. PMID 19019827 DOI: 10.1074/Jbc.M806312200  0.271
2012 Whitehead TA, Chevalier A, Song Y, Dreyfus C, Fleishman SJ, De Mattos C, Myers CA, Kamisetty H, Blair P, Wilson IA, Baker D. Optimization of affinity, specificity and function of designed influenza inhibitors using deep sequencing. Nature Biotechnology. 30: 543-8. PMID 22634563 DOI: 10.1038/Nbt.2214  0.271
2002 Schlosshauer M, Baker D. A General Expression for Bimolecular Association Rates with Orientational Constraints The Journal of Physical Chemistry B. 106: 12079-12083. DOI: 10.1021/Jp025894J  0.271
1997 Bolton C, O’Neill JK, Allen SJ, Baker D. Regulation of Chronic Relapsing Experimental Allergic Encephalomyelitis by Endogenous and Exogenous Glucocorticoids International Archives of Allergy and Immunology. 114: 74-80. PMID 9303334 DOI: 10.1159/000237646  0.271
2016 Koday MT, Nelson J, Chevalier A, Koday M, Kalinoski H, Stewart L, Carter L, Nieusma T, Lee PS, Ward AB, Wilson IA, Dagley A, Smee DF, Baker D, Fuller DH. A Computationally Designed Hemagglutinin Stem-Binding Protein Provides In Vivo Protection from Influenza Independent of a Host Immune Response. Plos Pathogens. 12: e1005409. PMID 26845438 DOI: 10.1371/Journal.Ppat.1005409  0.271
2008 Fan E, Baker D, Fields S, Gelb MH, Buckner FS, Van Voorhis WC, Phizicky E, Dumont M, Mehlin C, Grayhack E, Sullivan M, Verlinde C, Detitta G, Meldrum DR, Merritt EA, et al. Structural genomics of pathogenic protozoa: an overview. Methods in Molecular Biology (Clifton, N.J.). 426: 497-513. PMID 18542886 DOI: 10.1007/978-1-60327-058-8_33  0.27
2019 Cong Q, Anishchenko I, Ovchinnikov S, Baker D. Protein interaction networks revealed by proteome coevolution. Science (New York, N.Y.). 365: 185-189. PMID 31296772 DOI: 10.1126/Science.Aaw6718  0.27
2004 Baker DA, Kelly JM. Purine nucleotide cyclases in the malaria parasite. Trends in Parasitology. 20: 227-32. PMID 15105023 DOI: 10.1016/J.Pt.2004.02.007  0.27
2014 Kellogg EH, Alushin GM, Lander GC, Baker D, Nogales E. Studying the Structural Origins of Microtubule Dynamic Instability through Combining Computational Modeling and cryoEM Biophysical Journal. 106: 351a. DOI: 10.1016/J.Bpj.2013.11.1996  0.27
2006 de Lago E, Fernández-Ruiz J, Ortega-Gutiérrez S, Cabranes A, Pryce G, Baker D, López-Rodríguez M, Ramos JA. 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. European Neuropsychopharmacology : the Journal of the European College of Neuropsychopharmacology. 16: 7-18. PMID 16006105 DOI: 10.1016/J.Euroneuro.2005.06.001  0.27
2003 Morozov AV, Kortemme T, Baker D. Evaluation of models of electrostatic interactions in proteins Journal of Physical Chemistry B. 107: 2075-2090. DOI: 10.1021/Jp0267555  0.27
1998 Croxford JL, O'Neill JK, Ali RR, Browne K, Byrnes AP, Dallman MJ, Wood MJ, Fedlmann M, Baker D. Local gene therapy with CTLA4-immunoglobulin fusion protein in experimental allergic encephalomyelitis. European Journal of Immunology. 28: 3904-16. PMID 9862327 DOI: 10.1002/(Sici)1521-4141(199812)28:12<3904::Aid-Immu3904>3.0.Co;2-5  0.27
2011 Gront D, Kulp DW, Vernon RM, Strauss CE, Baker D. Generalized fragment picking in Rosetta: design, protocols and applications. Plos One. 6: e23294. PMID 21887241 DOI: 10.1371/Journal.Pone.0023294  0.27
2016 Mills JH, Sheffler W, Ener ME, Almhjell PJ, Oberdorfer G, Pereira JH, Parmeggiani F, Sankaran B, Zwart PH, Baker D. Computational design of a homotrimeric metalloprotein with a trisbipyridyl core. Proceedings of the National Academy of Sciences of the United States of America. PMID 27940918 DOI: 10.1073/Pnas.1600188113  0.27
2017 Anishchenko I, Ovchinnikov S, Kamisetty H, Baker D. Origins of coevolution between residues distant in protein 3D structures. Proceedings of the National Academy of Sciences of the United States of America. PMID 28784799 DOI: 10.1073/Pnas.1702664114  0.269
2014 Baker D, Amor S. Experimental autoimmune encephalomyelitis is a good model of multiple sclerosis if used wisely. Multiple Sclerosis and Related Disorders. 3: 555-64. PMID 26265267 DOI: 10.1016/J.Msard.2014.05.002  0.269
2008 Baker D, O'neill JK, Davison AN, Turk JL. Control of immune-mediated disease of the central nervous system requires the use of a neuroactive agent : elucidation by the action of mitoxantrone Clinical and Experimental Immunology. 90: 124-128. PMID 1395092 DOI: 10.1111/J.1365-2249.1992.Tb05843.X  0.269
2019 Pecora de Barros E, Schiffer JM, Vorobieva A, Dou J, Baker D, Amaro RE. Improving the Efficiency of Ligand-Binding Protein Design with Molecular Dynamics. Journal of Chemical Theory and Computation. PMID 31442033 DOI: 10.1021/Acs.Jctc.9B00483  0.269
2015 Baker D, Amor S. Mouse models of multiple sclerosis: lost in translation? Current Pharmaceutical Design. 21: 2440-52. PMID 25777759 DOI: 10.2174/1381612821666150316122706  0.269
1992 Baker D, Sohl JL, Agard DA. A protein-folding reaction under kinetic control. Nature. 356: 263-5. PMID 1552947 DOI: 10.1038/356263A0  0.269
2016 Reichen C, Hansen S, Forzani C, Honegger A, Fleishman SJ, Zhou T, Parmeggiani F, Ernst P, Madhurantakam C, Ewald C, Mittl PR, Zerbe O, Baker D, Caflisch A, Plückthun A. Computationally Designed Armadillo Repeat Proteins for Modular Peptide Recognition. Journal of Molecular Biology. PMID 27664438 DOI: 10.1016/J.Jmb.2016.09.012  0.269
2016 Bale JB, Gonen S, Liu Y, Sheffler W, Ellis D, Thomas C, Cascio D, Yeates TO, Gonen T, King NP, Baker D. Accurate design of megadalton-scale two-component icosahedral protein complexes. Science (New York, N.Y.). 353: 389-394. PMID 27463675 DOI: 10.1126/Science.Aaf8818  0.269
1999 Tsai J, Levitt M, Baker D. Hierarchy of structure loss in MD simulations of src SH3 domain unfolding. Journal of Molecular Biology. 291: 215-25. PMID 10438616 DOI: 10.1006/Jmbi.1999.2949  0.269
2002 Deng W, Baker DA. A novel cyclic GMP-dependent protein kinase is expressed in the ring stage of the Plasmodium falciparum life cycle. Molecular Microbiology. 44: 1141-51. PMID 12068803 DOI: 10.1046/J.1365-2958.2002.02948.X  0.268
2011 Khersonsky O, Röthlisberger D, Wollacott AM, Murphy P, Dym O, Albeck S, Kiss G, Houk KN, Baker D, Tawfik DS. Optimization of the in-silico-designed kemp eliminase KE70 by computational design and directed evolution. Journal of Molecular Biology. 407: 391-412. PMID 21277311 DOI: 10.1016/J.Jmb.2011.01.041  0.268
2017 Baker DA, Drought LG, Flueck C, Nofal SD, Patel A, Penzo M, Walker EM. Cyclic nucleotide signalling in malaria parasites. Open Biology. 7. PMID 29263246 DOI: 10.1098/Rsob.170213  0.268
2009 McRobert L, Taylor HM, Taylor CJ, Deng W, Moon RW, Fivelman QL, Grainger M, Polley SD, Sicard A, Billker O, Holder AA, Baker DA. The role of the cGMP-dependent protein kinase in development of the malaria parasite Bmc Pharmacology. 9: S2. DOI: 10.1186/1471-2210-9-S1-S2  0.268
2015 Matthaei JF, DiMaio F, Richards JJ, Pozzo LD, Baker D, Baneyx F. Designing Two-Dimensional Protein Arrays through Fusion of Multimers and Interface Mutations. Nano Letters. PMID 25986921 DOI: 10.1021/Acs.Nanolett.5B01499  0.268
2008 McBeth C, Seamons A, Pizarro JC, Fleishman SJ, Baker D, Kortemme T, Goverman JM, Strong RK. A new twist in TCR diversity revealed by a forbidden alphabeta TCR. Journal of Molecular Biology. 375: 1306-19. PMID 18155234 DOI: 10.1016/J.Jmb.2007.11.020  0.268
2009 DiMaio F, Tyka MD, Baker ML, Chiu W, Baker D. Refinement of protein structures into low-resolution density maps using rosetta. Journal of Molecular Biology. 392: 181-90. PMID 19596339 DOI: 10.1016/J.Jmb.2009.07.008  0.268
2011 Plet J, Wasson A, Ariel F, Le Signor C, Baker D, Mathesius U, Crespi M, Frugier F. MtCRE1-dependent cytokinin signaling integrates bacterial and plant cues to coordinate symbiotic nodule organogenesis in Medicago truncatula Plant Journal. 65: 622-633. PMID 21244535 DOI: 10.1111/J.1365-313X.2010.04447.X  0.268
2001 Baker D, Pryce G, Croxford JL, Brown P, Pertwee RG, Makriyannis A, Khanolkar A, Layward L, Fezza F, Bisogno T, Di Marzo V. Endocannabinoids control spasticity in a multiple sclerosis model The Faseb Journal : Official Publication of the Federation of American Societies For Experimental Biology. 15: 300-302. PMID 11156943 DOI: 10.1096/Fj.00-0399Fje  0.268
2012 Khare SD, Kipnis Y, Greisen P, Takeuchi R, Ashani Y, Goldsmith M, Song Y, Gallaher JL, Silman I, Leader H, Sussman JL, Stoddard BL, Tawfik DS, Baker D. Computational redesign of a mononuclear zinc metalloenzyme for organophosphate hydrolysis. Nature Chemical Biology. 8: 294-300. PMID 22306579 DOI: 10.1038/Nchembio.777  0.267
2005 Smith PA, Morris-Downes M, Heijmans N, Pryce G, Arter E, O'Neill JK, Hart B', Baker D, Amor S. Epitope spread is not critical for the relapse and progression of MOG 8-21 induced EAE in Biozzi ABH mice. Journal of Neuroimmunology. 164: 76-84. PMID 15927270 DOI: 10.1016/J.Jneuroim.2005.04.006  0.266
2019 Patel A, Perrin AJ, Flynn HR, Bisson C, Withers-Martinez C, Treeck M, Flueck C, Nicastro G, Martin SR, Ramos A, Gilberger TW, Snijders AP, Blackman MJ, Baker DA. Cyclic AMP signalling controls key components of malaria parasite host cell invasion machinery. Plos Biology. 17: e3000264. PMID 31075098 DOI: 10.1371/Journal.Pbio.3000264  0.266
2013 Bergeron JR, Worrall LJ, Sgourakis NG, DiMaio F, Pfuetzner RA, Felise HB, Vuckovic M, Yu AC, Miller SI, Baker D, Strynadka NC. A refined model of the prototypical Salmonella SPI-1 T3SS basal body reveals the molecular basis for its assembly. Plos Pathogens. 9: e1003307. PMID 23633951 DOI: 10.1371/Journal.Ppat.1003307  0.266
2013 Pryce G, Cabranes A, Fernández-Ruiz J, Bisogno T, Di Marzo V, Long JZ, Cravatt BF, Giovannoni G, Baker D. Control of experimental spasticity by targeting the degradation of endocannabinoids using selective fatty acid amide hydrolase inhibitors. Multiple Sclerosis (Houndmills, Basingstoke, England). 19: 1896-904. PMID 23625705 DOI: 10.1177/1352458513485982  0.266
2008 Pinteaux-Jones F, Sevastou IG, Fry VA, Heales S, Baker D, Pocock JM. Myelin-induced microglial neurotoxicity can be controlled by microglial metabotropic glutamate receptors. Journal of Neurochemistry. 106: 442-54. PMID 18419765 DOI: 10.1111/J.1471-4159.2008.05426.X  0.266
2011 Koga N, Koga(Tatsumi) R, Liu G, Xiao R, Montelione GT, Baker D. 1SB-01 Computational De Novo Design of Protein Structures(1SB Exploring design principles of life,The 49th Annual Meeting of the Biophysical Society of Japan) Seibutsu Butsuri. 51: S2. DOI: 10.2142/Biophys.51.S2_1  0.266
2020 Wu HQ, Baker D, Ovaa H. Small molecules that target the ubiquitin system. Biochemical Society Transactions. PMID 32196552 DOI: 10.1042/Bst20190535  0.265
2011 Li M, Dimaio F, Zhou D, Gustchina A, Lubkowski J, Dauter Z, Baker D, Wlodawer A. Crystal structure of XMRV protease differs from the structures of other retropepsins. Nature Structural & Molecular Biology. 18: 227-9. PMID 21258323 DOI: 10.1038/Nsmb.1964  0.265
2012 Sher F, Amor S, Gerritsen W, Baker D, Jackson SL, Boddeke E, Copray S. Intraventricularly injected Olig2-NSCs attenuate established relapsing-remitting EAE in mice. Cell Transplantation. 21: 1883-97. PMID 22469520 DOI: 10.3727/096368911X637443  0.265
2008 Röthlisberger D, Khersonsky O, Wollacott AM, Jiang L, DeChancie J, Betker J, Gallaher JL, Althoff EA, Zanghellini A, Dym O, Albeck S, Houk KN, Tawfik DS, Baker D. Kemp elimination catalysts by computational enzyme design. Nature. 453: 190-5. PMID 18354394 DOI: 10.1038/Nature06879  0.265
2013 DiMaio F, Echols N, Headd JJ, Terwilliger TC, Adams PD, Baker D. Improved low-resolution crystallographic refinement with Phenix and Rosetta. Nature Methods. 10: 1102-4. PMID 24076763 DOI: 10.1107/S2053273314092171  0.265
2020 VanAernum ZL, Busch F, Jones BJ, Jia M, Chen Z, Boyken SE, Sahasrabuddhe A, Baker D, Wysocki VH. Rapid online buffer exchange for screening of proteins, protein complexes and cell lysates by native mass spectrometry. Nature Protocols. PMID 32005983 DOI: 10.1038/S41596-019-0281-0  0.265
2017 Lin YR, Koga N, Vorobiev SM, Baker D. Cyclic oligomer design with de novo αβ-proteins. Protein Science : a Publication of the Protein Society. PMID 28801928 DOI: 10.1002/Pro.3270  0.265
2004 Morozov AV, Kortemme T, Tsemekhman K, Baker D. 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. 101: 6946-51. PMID 15118103 DOI: 10.1073/Pnas.0307578101  0.265
2007 Yatsenko AS, Gray EE, Shcherbata HR, Patterson LB, Sood VD, Kucherenko MM, Baker D, Ruohola-Baker H. 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. The Journal of Biological Chemistry. 282: 15159-69. PMID 17355978 DOI: 10.1074/Jbc.M608800200  0.265
2000 Thayer EC, Bystroff C, Baker D. Detection of protein coding sequences using a mixture model for local protein amino acid sequence. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 7: 317-27. PMID 10890405 DOI: 10.1089/10665270050081559  0.265
2012 Richter F, Blomberg R, Khare SD, Kiss G, Kuzin AP, Smith AJ, Gallaher J, Pianowski Z, Helgeson RC, Grjasnow A, Xiao R, Seetharaman J, Su M, Vorobiev S, Lew S, ... ... Baker D, et al. Computational design of catalytic dyads and oxyanion holes for ester hydrolysis. Journal of the American Chemical Society. 134: 16197-206. PMID 22871159 DOI: 10.1021/Ja3037367  0.265
2016 Berger S, Procko E, Margineantu D, Lee EF, Shen BW, Zelter A, Silva DA, Chawla K, Herold MJ, Garnier JM, Johnson R, MacCoss MJ, Lessene G, Davis TN, Stayton PS, ... ... Baker D, et al. Computationally designed high specificity inhibitors delineate the roles of BCL2 family proteins in cancer. Elife. 5. PMID 27805565 DOI: 10.7554/Elife.20352  0.264
2012 Gnanapavan S, Grant D, Pryce G, Jackson S, Baker D, Giovannoni G. Neurofilament a biomarker of neurodegeneration in autoimmune encephalomyelitis. Autoimmunity. 45: 298-303. PMID 22276904 DOI: 10.3109/08916934.2012.654865  0.264
2013 Vernon R, Shen Y, Baker D, Lange OF. Improved chemical shift based fragment selection for CS-Rosetta using Rosetta3 fragment picker. Journal of Biomolecular Nmr. 57: 117-27. PMID 23975356 DOI: 10.1007/S10858-013-9772-4  0.264
2008 Das R, Kudaravalli M, Jonikas M, Laederach A, Fong R, Schwans JP, Baker D, Piccirilli JA, Altman RB, Herschlag D. 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. 105: 4144-9. PMID 18322008 DOI: 10.1073/Pnas.0709032105  0.264
2017 Strauch EM, Bernard SM, La D, Bohn AJ, Lee PS, Anderson CE, Nieusma T, Holstein CA, Garcia NK, Hooper KA, Ravichandran R, Nelson JW, Sheffler W, Bloom JD, Lee KK, ... ... Baker D, et al. Computational design of trimeric influenza-neutralizing proteins targeting the hemagglutinin receptor binding site. Nature Biotechnology. PMID 28604661 DOI: 10.1038/Nbt.3907  0.264
2003 Muhia DK, Swales CA, Eckstein-Ludwig U, Saran S, Polley SD, Kelly JM, Schaap P, Krishna S, Baker DA. Multiple splice variants encode a novel adenylyl cyclase of possible plastid origin expressed in the sexual stage of the malaria parasite Plasmodium falciparum. The Journal of Biological Chemistry. 278: 22014-22. PMID 12668669 DOI: 10.1074/Jbc.M301639200  0.264
2002 Morris-Downes MM, Smith PA, Rundle JL, Piddlesden SJ, Baker D, Pham-Dinh D, Heijmans N, Amor S. Pathological and regulatory effects of anti-myelin antibodies in experimental allergic encephalomyelitis in mice. Journal of Neuroimmunology. 125: 114-24. PMID 11960647 DOI: 10.1016/S0165-5728(02)00040-1  0.263
1998 Triantaphyllopoulos K, Croxford J, Baker D, Chernajovsky Y. Cloning and expression of murine IFN beta and a TNF antagonist for gene therapy of experimental allergic encephalomyelitis. Gene Therapy. 5: 253-263. PMID 9578846 DOI: 10.1038/Sj.Gt.3300570  0.263
2018 Lau YK, Baytshtok V, Howard TA, Fiala BM, Morgan JM, Carter LP, Baker D, Lima CD, Bahl CD. Discovery and engineering of enhanced SUMO protease enzymes. The Journal of Biological Chemistry. PMID 29976752 DOI: 10.1074/Jbc.Ra118.004146  0.263
2019 Baker D. Computationally designed protein activation National Science Review. 6: 609-610. DOI: 10.1093/Nsr/Nwz063  0.263
2020 Xu C, Lu P, Gamal El-Din TM, Pei XY, Johnson MC, Uyeda A, Bick MJ, Xu Q, Jiang D, Bai H, Reggiano G, Hsia Y, Brunette TJ, Dou J, Ma D, ... ... Baker D, et al. Computational design of transmembrane pores. Nature. PMID 32848250 DOI: 10.1038/S41586-020-2646-5  0.262
1997 Rank JA, Baker D. A desolvation barrier to hydrophobic cluster formation may contribute to the rate-limiting step in protein folding Protein Science. 6: 347-354. PMID 9041636 DOI: 10.1002/Pro.5560060210  0.262
2014 Mazor R, Eberle JA, Hu X, Vassall AN, Onda M, Beers R, Lee EC, Kreitman RJ, Lee B, Baker D, King C, Hassan R, Benhar I, Pastan I. 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. 111: 8571-6. PMID 24799704 DOI: 10.1073/Pnas.1405153111  0.262
1994 Baker D, Butler D, O'Neill JK, Turk JL, Feldman M. Inhibition of EAE by TNF-receptor fusion proteins Journal of Neuroimmunology. 54: 151. DOI: 10.1016/0165-5728(94)90254-2  0.262
2003 Pryce G, Ahmed Z, Hankey DJ, Jackson SJ, Croxford JL, Pocock JM, Ledent C, Petzold A, Thompson AJ, Giovannoni G, Cuzner ML, Baker D. Cannabinoids inhibit neurodegeneration in models of multiple sclerosis. Brain : a Journal of Neurology. 126: 2191-202. PMID 12876144 DOI: 10.1093/Brain/Awg224  0.262
2009 Zhu J, Luo BH, Barth P, Schonbrun J, Baker D, Springer TA. The structure of a receptor with two associating transmembrane domains on the cell surface: integrin alphaIIbbeta3. Molecular Cell. 34: 234-49. PMID 19394300 DOI: 10.1016/J.Molcel.2009.02.022  0.262
2019 Foight GW, Wang Z, Wei CT, Jr Greisen P, Warner KM, Cunningham-Bryant D, Park K, Brunette TJ, Sheffler W, Baker D, Maly DJ. Multi-input chemical control of protein dimerization for programming graded cellular responses. Nature Biotechnology. PMID 31501561 DOI: 10.1038/S41587-019-0242-8  0.262
2012 Kipp M, van der Star B, Vogel DY, Puentes F, van der Valk P, Baker D, Amor S. Experimental in vivo and in vitro models of multiple sclerosis: EAE and beyond. Multiple Sclerosis and Related Disorders. 1: 15-28. PMID 25876447 DOI: 10.1016/J.Msard.2011.09.002  0.262
2015 O'Meara MJ, Leaver-Fay A, Tyka M, Stein A, Houlihan K, DiMaio F, Bradley P, Kortemme T, Baker D, Snoeyink J, Kuhlman B. A Combined Covalent-Electrostatic Model of Hydrogen Bonding Improves Structure Prediction with Rosetta. Journal of Chemical Theory and Computation. 11: 609-622. PMID 25866491 DOI: 10.1021/Ct500864R  0.262
2000 Carucci DJ, Witney AA, Muhia DK, Warhurst DC, Schaap P, Meima M, Li JL, Taylor MC, Kelly JM, Baker DA. Guanylyl cyclase activity associated with putative bifunctional integral membrane proteins in Plasmodium falciparum. The Journal of Biological Chemistry. 275: 22147-56. PMID 10747978 DOI: 10.1074/Jbc.M001021200  0.262
2010 Smagghe BJ, Huang PS, Ban YE, Baker D, Springer TA. Modulation of integrin activation by an entropic spring in the {beta}-knee. The Journal of Biological Chemistry. 285: 32954-66. PMID 20670939 DOI: 10.1074/Jbc.M110.145177  0.261
2012 Star BJvd, Vogel DYS, Kipp M, Puentes F, Baker D, Amor S. In vitro and in vivo models of multiple sclerosis Cns & Neurological Disorders-Drug Targets. 11: 570-588. PMID 22583443 DOI: 10.2174/187152712801661284  0.261
2001 Li JL, Targett GA, Baker DA. Primary structure and sexual stage-specific expression of a LAMMER protein kinase of Plasmodium falciparum. International Journal For Parasitology. 31: 387-92. PMID 11306117 DOI: 10.1016/S0020-7519(01)00126-6  0.261
2014 van den Elsen PJ, van Eggermond MC, Puentes F, van der Valk P, Baker D, Amor S. The epigenetics of multiple sclerosis and other related disorders. Multiple Sclerosis and Related Disorders. 3: 163-75. PMID 25878004 DOI: 10.1016/J.Msard.2013.08.007  0.261
2001 Hankey DJ, Nickerson JM, Donoso LA, Lightman SL, Baker D. Experimental autoimmune uveoretinitis in mice (Biozzi ABH and NOD) expressing the autoimmune-associated H-2A(g7) molecule: identification of a uveitogenic epitope. Journal of Neuroimmunology. 118: 212-22. PMID 11498256 DOI: 10.1016/S0165-5728(01)00341-1  0.261
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