Center-Authored Papers

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Journal Article
Drew K, Renfrew DP, Craven TW, Butterfoss GL, Chou F-C, Lyskov S, Bullock BN, Watkins A, Labonte JW, Pacella M et al..  2013.  Adding diverse noncanonical backbones to rosetta: enabling peptidomimetic design.. PloS one. 8(7):e67051. Abstract
Liu LA, Bradley P.  2012.  Atomistic modeling of protein-DNA interaction specificity: progress and applications.. Current opinion in structural biology. 22(4):397-405. Abstract
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
Mak AN-S, Bradley P, Cernadas RA, Bogdanove AJ, Stoddard BL.  2012.  The Crystal Structure of TAL Effector PthXo1 Bound to Its DNA Target.. Science (New York, N.Y.). 335(6069):716-719. 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
Yanover C, Bradley P.  2011.  Extensive protein and DNA backbone sampling improves structure-based specificity prediction for C2H2 zinc fingers.. Nucleic acids research. 39(11):4564-76. Abstract
Yanover C, Petersdorf EW, Bradley P.  2011.  HLA mismatches and hematopoietic cell transplantation: structural simulations assess the impact of changes in peptide binding specificity on transplant outcome.. Immunome research. 7(2):24. 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
Zaslavsky E, Bradley P, Yanover C.  2010.  Inferring PDZ domain multi-mutant binding preferences from single-mutant data.. PloS one. 5(9):e12787. Abstract
Keating R, Hertz T, Wehenkel M, Harris TL, Edwards BA, McClaren JL, Brown SA, Surman S, Wilson ZS, Bradley P et al..  2013.  The kinase mTOR modulates the antibody response to provide cross-protective immunity to lethal infection with influenza virus.. Nature immunology. 14(12):1266-76. Abstract
Yanover C, Bradley P.  2011.  Large-scale characterization of peptide-MHC binding landscapes with structural simulations.. Proceedings of the National Academy of Sciences of the United States of America. 108(17):6981-6. Abstract
Zhang GL, Ansari HR, Bradley P, Cawley GC, Hertz T, Hu X, Jojic N, Kim Y, Kohlbacher O, Lund O et al..  2011.  Machine learning competition in immunology - Prediction of HLA class I binding peptides.. Journal of immunological methods. 374(1-2):1-4.
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
Li S, Bradley P.  2013.  Probing the role of interfacial waters in protein-DNA recognition using a hybrid implicit/explicit solvation model.. Proteins. Abstract
Dash P, Fiore-Gartland AJ, Hertz T, Wang GC, Sharma S, Souquette A, Crawford JC, Clemens BE, Nguyen THO, Kedzierska K et al..  2017.  Quantifiable predictive features define epitope-specific T cell receptor repertoires.. Nature. Abstract
McCoy CO, Bedford T, Minin VN, Bradley P, Robins H, Matsen FA.  2015.  Quantifying evolutionary constraints on B-cell affinity maturation.. Philosophical transactions of the Royal Society of London. Series B, Biological sciences. 370(1676) Abstract
Doyle L, Hallinan J, Bolduc J, Parmeggiani F, Baker D, Stoddard BL, Bradley P.  2015.  Rational design of α-helical tandem repeat proteins with closed architectures.. Nature. 528(7583):585-8. Abstract
Alford RF, Leaver-Fay A, Jeliazkov JR, O'Meara MJ, DiMaio FP, Park H, Shapovalov MV, Renfrew DP, Mulligan VK, Kappel K et al..  2017.  The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design.. Journal of chemical theory and computation. 13(6):3031-3048. 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
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
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
Park H, Bradley P, Greisen P, Liu Y, Mulligan VK, Kim DE, Baker D, DiMaio F.  2016.  Simultaneous Optimization of Biomolecular Energy Functions on Features from Small Molecules and Macromolecules.. Journal of chemical theory and computation. 12(12):6201-6212. Abstract
Bradley P.  2012.  Structural modeling of TAL effector-DNA interactions.. Protein science : a publication of the Protein Society. 21(4):471-4. Abstract
Joyce AP, Zhang C, Bradley P, Havranek JJ.  2015.  Structure-based modeling of protein: DNA specificity.. Briefings in functional genomics. 14(1):39-49. Abstract
King CA, Bradley P.  2010.  Structure-based prediction of protein-peptide specificity in Rosetta.. Proteins. 78(16):3437-49. Abstract