Center-Authored Papers

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2008
Jiang L, Althoff EA, Clemente FR, Doyle L, Röthlisberger D, Zanghellini A, Gallaher JL, Betker JL, Tanaka F, Barbas CF et al..  2008.  De novo computational design of retro-aldol enzymes.. Science (New York, N.Y.). 319(5868):1387-91. Abstract
André I, Strauss CEM, Kaplan DB, Bradley P, Baker D.  2008.  Emergence of symmetry in homooligomeric biological assemblies.. Proceedings of the National Academy of Sciences of the United States of America. 105(42):16148-52. Abstract
McBeth C, Seamons A, Pizarro JC, Fleishman SJ, Baker D, Kortemme T, Goverman JM, Strong RK.  2008.  A new twist in TCR diversity revealed by a forbidden alphabeta TCR.. Journal of molecular biology. 375(5):1306-19. Abstract
2009
Thyme SB, Jarjour J, Takeuchi R, Havranek JJ, Ashworth J, Scharenberg AM, Stoddard BL, Baker D.  2009.  Exploitation of binding energy for catalysis and design.. Nature. 461(7268):1300-4. Abstract
Kim DE, Blum B, Bradley P, Baker D.  2009.  Sampling bottlenecks in de novo protein structure prediction.. Journal of molecular biology. 393(1):249-60. Abstract
Murphy PM, Bolduc JM, Gallaher JL, Stoddard BL, Baker D.  2009.  Alteration of enzyme specificity by computational loop remodeling and design.. Proceedings of the National Academy of Sciences of the United States of America. 106(23):9215-20. Abstract
2010
Ashworth J, Taylor GK, Havranek JJ, Quadri AS, Stoddard BL, Baker D.  2010.  Computational reprogramming of homing endonuclease specificity at multiple adjacent base pairs.. Nucleic acids research. 38(16):5601-8. Abstract
Fleishman SJ, Corn JE, Strauch EM, Whitehead TA, Andre I, Thompson J, Havranek JJ, Das R, Bradley P, Baker D.  2010.  Rosetta in CAPRI rounds 13-19.. Proteins. 78(15):3212-8. Abstract
Siegel JB, Zanghellini A, Lovick HM, Kiss G, Lambert AR, St Clair JL, Gallaher JL, Hilvert D, Gelb MH, Stoddard BL et al..  2010.  Computational design of an enzyme catalyst for a stereoselective bimolecular Diels-Alder reaction.. Science (New York, N.Y.). 329(5989):309-13. Abstract
Correia BE, Ban Y-EA, Holmes MA, Xu H, Ellingson K, Kraft Z, Carrico C, Boni E, Sather ND, Zenobia C et al..  2010.  Computational design of epitope-scaffolds allows induction of antibodies specific for a poorly immunogenic HIV vaccine epitope.. Structure (London, England : 1993). 18(9):1116-26. Abstract
2011
Leaver-Fay A, Tyka M, Lewis SM, Lange OF, Thompson J, Jacak R, Kaufman K, Renfrew DP, Smith CA, Sheffler W et al..  2011.  ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules.. Methods in enzymology. 487:545-74. Abstract
Brzovic PS, Heikaus CC, Kisselev L, Vernon R, Herbig E, Pacheco D, Warfield L, Littlefield P, Baker D, Klevit RE et al..  2011.  The acidic transcription activator gcn4 binds the mediator subunit gal11/med15 using a simple protein interface forming a fuzzy complex.. Molecular cell. 44(6):942-53. Abstract
Azoitei ML, Correia BE, Ban Y-EA, Carrico C, Kalyuzhniy O, Chen L, Schroeter A, Huang P-S, McLellan JS, Kwong PD et al..  2011.  Computation-guided backbone grafting of a discontinuous motif onto a protein scaffold.. Science (New York, N.Y.). 334(6054):373-6. Abstract
2012
Khare SD, Kipnis Y, Greisen PJ, Takeuchi R, Ashani Y, Goldsmith M, Song Y, Gallaher JL, Silman I, Leader H et al..  2012.  Computational redesign of a mononuclear zinc metalloenzyme for organophosphate hydrolysis.. Nature chemical biology. 8(3):294-300. Abstract
Baxter S, Lambert AR, Kuhar R, Jarjour J, Kulshina N, Parmeggiani F, Danaher P, Gano J, Baker D, Stoddard BL et al..  2012.  Engineering domain fusion chimeras from I-OnuI family LAGLIDADG homing endonucleases.. Nucleic acids research. Abstract
Thyme SB, Baker D, Bradley P.  2012.  Improved Modeling of Side-Chain-Base Interactions and Plasticity in Protein-DNA Interface Design.. Journal of molecular biology. 419(3-4):255-74. Abstract
Wang L, Althoff EA, Bolduc J, Jiang L, Moody J, Lassila JK, Giger L, Hilvert D, Stoddard BL, Baker D.  2012.  Structural Analyses of Covalent Enzyme-Substrate Analog Complexes Reveal the Strengths and Limitations of De Novo Enzyme Design.. Journal of molecular biology. 415(3):615-625. Abstract
Eiben CB, Siegel JB, Bale JB, Cooper S, Khatib F, Shen BW, Players F, Stoddard BL, Popovic Z, Baker D.  2012.  Increased Diels-Alderase activity through backbone remodeling guided by Foldit players.. Nature biotechnology. 30(2):190-2. Abstract
2013
Mills JH, Khare SD, Bolduc JM, Forouhar F, Mulligan VK, Lew S, Seetharaman J, Tong L, Stoddard BL, Baker D.  2013.  Computational design of an unnatural amino Acid dependent metalloprotein with atomic level accuracy.. Journal of the American Chemical Society. 135(36):13393-9. Abstract
Boissel S, Jarjour J, Astrakhan A, Adey A, Gouble A, Duchateau P, Shendure J, Stoddard BL, Certo MT, Baker D et al..  2014.  megaTALs: a rare-cleaving nuclease architecture for therapeutic genome engineering.. Nucleic acids research. 42(4):2591-601. Abstract
Tinberg CE, Khare SD, Dou J, Doyle L, Nelson JW, Schena A, Jankowski W, Kalodimos CG, Johnsson K, Stoddard BL et al..  2013.  Computational design of ligand-binding proteins with high affinity and selectivity.. Nature. 501(7466):212-6. Abstract
2014
Procko E, Berguig GY, Shen BW, Song Y, Frayo S, Convertine AJ, Margineantu D, Booth G, Correia BE, Cheng Y et al..  2014.  A computationally designed inhibitor of an epstein-barr viral bcl-2 protein induces apoptosis in infected cells.. Cell. 157(7):1644-56. Abstract
Correia BE, Bates JT, Loomis RJ, Baneyx G, Carrico C, Jardine JG, Rupert P, Correnti C, Kalyuzhniy O, Vittal V et al..  2014.  Proof of principle for epitope-focused vaccine design.. Nature. Abstract
261
Mills JH, Khare SD, Bolduc JM, Forouhar F, Mulligan VK, Lew S, Seetharaman J, Tong L, Stoddard BL, Baker D.  2013.  Computational design of an unnatural amino Acid dependent metalloprotein with atomic level accuracy.. Journal of the American Chemical Society. 135(36):13393-9. Abstract
336
Eiben CB, Siegel JB, Bale JB, Cooper S, Khatib F, Shen BW, Players F, Stoddard BL, Popovic Z, Baker D.  2012.  Increased Diels-Alderase activity through backbone remodeling guided by Foldit players.. Nature biotechnology. 30(2):190-2. Abstract