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Phil Bradley - Publications

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35 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Leman JK, Weitzner BD, Lewis SM, Adolf-Bryfogle J, Alam N, Alford RF, Aprahamian M, Baker D, Barlow KA, Barth P, Basanta B, Bender BJ, Blacklock K, Bonet J, Boyken SE, ... Bradley P, et al. Macromolecular modeling and design in Rosetta: recent methods and frameworks. Nature Methods. PMID 32483333 DOI: 10.1038/S41592-020-0848-2  0.685
2020 Koehler Leman J, Weitzner BD, Renfrew PD, Lewis SM, Moretti R, Watkins AM, Mulligan VK, Lyskov S, Adolf-Bryfogle J, Labonte JW, Krys J, Bystroff C, Schief W, Gront D, ... ... Bradley P, et al. Better together: Elements of successful scientific software development in a distributed collaborative community. Plos Computational Biology. 16: e1007507. PMID 32365137 DOI: 10.1371/Journal.Pcbi.1007507  0.757
2019 Kuhlman B, Bradley P. Advances in protein structure prediction and design. Nature Reviews. Molecular Cell Biology. PMID 31417196 DOI: 10.1038/S41580-019-0163-X  0.644
2018 Shen BW, Doyle L, Bradley P, Heiter DF, Lunnen KD, Wilson GG, Stoddard BL. Structure, subunit organization and behavior of the asymmetric Type IIT restriction endonuclease BbvCI. Nucleic Acids Research. PMID 30395313 DOI: 10.2210/Pdb6Maf/Pdb  0.321
2017 Crook ZR, Sevilla GP, Friend D, Brusniak MY, Bandaranayake AD, Clarke M, Gewe M, Mhyre AJ, Baker D, Strong RK, Bradley P, Olson JM. Mammalian display screening of diverse cystine-dense peptides for difficult to drug targets. Nature Communications. 8: 2244. PMID 29269835 DOI: 10.1038/S41467-017-02098-8  0.309
2017 Alford RF, Leaver-Fay A, Jeliazkov JR, O'Meara MJ, DiMaio FP, Park H, Shapovalov MV, Renfrew PD, Mulligan VK, Kappel K, Labonte JW, Pacella MS, Bonneau R, Bradley P, Dunbrack RL, et al. The Rosetta all-atom energy function for macromolecular modeling and design. Journal of Chemical Theory and Computation. PMID 28430426 DOI: 10.1021/Acs.Jctc.7B00125  0.789
2016 Park H, Bradley P, Greisen P, Liu Y, Mulligan VK, Kim DE, Baker D, DiMaio F. Simultaneous optimization of biomolecular energy function on features from small molecules and macromolecules. Journal of Chemical Theory and Computation. PMID 27766851 DOI: 10.1021/Acs.Jctc.6B00819  0.539
2015 Doyle L, Hallinan J, Bolduc J, Parmeggiani F, Baker D, Stoddard BL, Bradley P. Rational design of α-helical tandem repeat proteins with closed architectures. Nature. PMID 26675735 DOI: 10.1038/Nature16191  0.463
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  0.787
2015 Joyce AP, Zhang C, Bradley P, Havranek JJ. Structure-based modeling of protein: DNA specificity. Briefings in Functional Genomics. 14: 39-49. PMID 25414269 DOI: 10.1093/Bfgp/Elu044  0.614
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  0.766
2013 Drew K, Renfrew PD, Craven TW, Butterfoss GL, Chou FC, Lyskov S, Bullock BN, Watkins A, Labonte JW, Pacella M, Kilambi KP, Leaver-Fay A, Kuhlman B, Gray JJ, Bradley P, et al. Adding diverse noncanonical backbones to rosetta: enabling peptidomimetic design. Plos One. 8: e67051. PMID 23869206 DOI: 10.1371/Journal.Pone.0067051  0.818
2012 Liu LA, Bradley P. Atomistic modeling of protein-DNA interaction specificity: Progress and applications Current Opinion in Structural Biology. 22: 397-405. PMID 22796087 DOI: 10.1016/j.sbi.2012.06.002  0.365
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  0.763
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  0.825
2011 Yanover C, Bradley P. Extensive protein and DNA backbone sampling improves structure-based specificity prediction for C2H2 zinc fingers Nucleic Acids Research. 39: 4564-4576. PMID 21343182 DOI: 10.1093/nar/gkr048  0.339
2011 Leaver-Fay A, Tyka M, Lewis SM, Lange OF, Thompson J, Jacak R, Kaufman K, Renfrew PD, Smith CA, Sheffler W, Davis IW, Cooper S, Treuille A, Mandell DJ, Richter F, ... ... Bradley P, et al. ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules. Methods in Enzymology. 487: 545-74. PMID 21187238 DOI: 10.1016/B978-0-12-381270-4.00019-6  0.735
2010 King CA, Bradley P. Structure-based prediction of protein-peptide specificity in rosetta Proteins: Structure, Function and Bioinformatics. 78: 3437-3449. PMID 20954182 DOI: 10.1002/prot.22851  0.576
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  0.788
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  0.464
2009 Blum B, Jordan MI, Kim DE, Das R, Bradley P, Baker D. Feature selection methods for improving protein structure prediction with Rosetta Advances in Neural Information Processing Systems 20 - Proceedings of the 2007 Conference.  0.533
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  0.617
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  0.723
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  0.737
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, 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  0.773
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  0.551
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  0.802
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  0.378
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  0.821
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  0.818
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  0.789
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  0.44
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  0.81
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  0.772
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  0.821
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