Center-Authored Papers

Filters: Author is Baker, David  [Clear All Filters]
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Bhardwaj G, Mulligan VK, Bahl CD, Gilmore JM, Harvey PJ, Cheneval O, Buchko GW, Pulavarti SVSRK, Kaas Q, Eletsky A et al..  2016.  Accurate de novo design of hyperstable constrained peptides.. Nature. 538(7625):329-335. 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
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
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O'Meara MJ, Leaver-Fay A, Tyka M, Stein A, Houlihan K, DiMaio F, Bradley P, Kortemme T, Baker D, Snoeyink J et al..  2015.  A Combined Covalent-Electrostatic Model of Hydrogen Bonding Improves Structure Prediction with Rosetta.. Journal of chemical theory and computation. 11(2):609-622. 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
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
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
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
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
Strauch E-M, Bernard SM, La D, Bohn AJ, Lee PS, Anderson CE, Nieusma T, Holstein CA, Garcia NK, Hooper KA et al..  2017.  Computational design of trimeric influenza-neutralizing proteins targeting the hemagglutinin receptor binding site.. Nature biotechnology. Abstract
Siegel JB, Smith AL, Poust S, Wargacki AJ, Bar-Even A, Louw C, Shen BW, Eiben CB, Tran HM, Noor E et al..  2015.  Computational protein design enables a novel one-carbon assimilation pathway.. Proceedings of the National Academy of Sciences of the United States of America. 112(12):3704-9. Abstract
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
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
Berger S, Procko E, Margineantu D, Lee EF, Shen BW, Zelter A, Silva D-A, Chawla K, Herold MJ, Garnier J-M et al..  2016.  Computationally designed high specificity inhibitors delineate the roles of BCL2 family proteins in cancer.. eLife. 5 Abstract
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
Park K, Shen BW, Parmeggiani F, Huang P-S, Stoddard BL, Baker D.  2015.  Control of repeat-protein curvature by computational protein design.. Nature structural & molecular biology. 22(2):167-74. Abstract
Smith RD, Damm-Ganamet KL, Dunbar JB, Ahmed A, Chinnaswamy K, Delproposto JE, Kubish GM, Tinberg CE, Khare SD, Dou J et al..  2016.  CSAR Benchmark Exercise 2013: Evaluation of Results from a Combined Computational Protein Design, Docking, and Scoring/Ranking Challenge.. Journal of chemical information and modeling. 56(6):1022-1031. Abstract
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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
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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
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, 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
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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
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
Berguig GY, Convertine AJ, Frayo S, Kern HB, Procko E, Roy D, Srinivasan S, Margineantu DH, Booth G, Palanca-Wessels MC et al..  2015.  Intracellular delivery system for antibody-Peptide drug conjugates.. Molecular therapy : the journal of the American Society of Gene Therapy. 23(5):907-17. Abstract
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Thyme SB, Song Y, Brunette TJ, Szeto MD, Kusak L, Bradley P, Baker D.  2014.  Massively parallel determination and modeling of endonuclease substrate specificity.. Nucleic acids research. 42(22):13839-52. Abstract