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Philip Bradley
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ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules
A Leaver-Fay, M Tyka, SM Lewis, OF Lange, J Thompson, R Jacak, ...
Methods in enzymology 487, 545-574, 2011
17382011
Toward high-resolution de novo structure prediction for small proteins
P Bradley, KMS Misura, D Baker
Science 309 (5742), 1868-1871, 2005
10612005
The Rosetta all-atom energy function for macromolecular modeling and design
RF Alford, A Leaver-Fay, JR Jeliazkov, MJ O’Meara, FP DiMaio, H Park, ...
Journal of chemical theory and computation 13 (6), 3031-3048, 2017
8752017
The crystal structure of TAL effector PthXo1 bound to its DNA target
ANS Mak, P Bradley, RA Cernadas, AJ Bogdanove, BL Stoddard
Science 335 (6069), 716-719, 2012
6782012
Quantifiable predictive features define epitope-specific T cell receptor repertoires
P Dash, AJ Fiore-Gartland, T Hertz, GC Wang, S Sharma, A Souquette, ...
Nature 547 (7661), 89-93, 2017
5402017
Protein–protein docking with backbone flexibility
C Wang, P Bradley, D Baker
Journal of molecular biology 373 (2), 503-519, 2007
4532007
Advances in protein structure prediction and design
B Kuhlman, P Bradley
Nature Reviews Molecular Cell Biology 20 (11), 681-697, 2019
3922019
High-resolution structure prediction and the crystallographic phase problem
B Qian, S Raman, R Das, P Bradley, AJ McCoy, RJ Read, D Baker
Nature 450 (7167), 259-264, 2007
3742007
Progress in modeling of protein structures and interactions
O Schueler-Furman, C Wang, P Bradley, K Misura, D Baker
science 310 (5748), 638-642, 2005
3652005
Automated prediction of CASP‐5 structures using the Robetta server
D Chivian, DE Kim, L Malmström, P Bradley, T Robertson, P Murphy, ...
Proteins: Structure, Function, and Bioinformatics 53 (S6), 524-533, 2003
3522003
Assigning function to yeast proteins by integration of technologies
TR Hazbun, L Malmström, S Anderson, BJ Graczyk, B Fox, M Riffle, ...
Molecular cell 12 (6), 1353-1365, 2003
3312003
De novo prediction of three-dimensional structures for major protein families
R Bonneau, CEM Strauss, CA Rohl, D Chivian, P Bradley, L Malmström, ...
Journal of molecular biology 322 (1), 65-78, 2002
3192002
Macromolecular modeling and design in Rosetta: recent methods and frameworks
JK Leman, BD Weitzner, SM Lewis, J Adolf-Bryfogle, N Alam, RF Alford, ...
Nature methods 17 (7), 665-680, 2020
2992020
Simultaneous optimization of biomolecular energy functions on features from small molecules and macromolecules
H Park, P Bradley, P Greisen Jr, Y Liu, VK Mulligan, DE Kim, D Baker, ...
Journal of chemical theory and computation 12 (12), 6201-6212, 2016
2942016
U2AF1 mutations alter splice site recognition in hematological malignancies
JO Ilagan, A Ramakrishnan, B Hayes, ME Murphy, AS Zebari, P Bradley, ...
Genome research 25 (1), 14-26, 2015
2712015
Structure prediction for CASP7 targets using extensive all‐atom refinement with Rosetta@ home
R Das, B Qian, S Raman, R Vernon, J Thompson, P Bradley, S Khare, ...
Proteins: Structure, Function, and Bioinformatics 69 (S8), 118-128, 2007
2612007
Rosetta predictions in CASP5: successes, failures, and prospects for complete automation
P Bradley, D Chivian, J Meiler, KMS Misura, CA Rohl, WR Schief, ...
Proteins: Structure, Function, and Bioinformatics 53 (S6), 457-468, 2003
2432003
Combined covalent-electrostatic model of hydrogen bonding improves structure prediction with Rosetta
MJ O’Meara, A Leaver-Fay, MD Tyka, A Stein, K Houlihan, F DiMaio, ...
Journal of chemical theory and computation 11 (2), 609-622, 2015
2192015
Modeling symmetric macromolecular structures in Rosetta3
F DiMaio, A Leaver-Fay, P Bradley, D Baker, I André
PloS one 6 (6), e20450, 2011
2092011
Free modeling with Rosetta in CASP6
P Bradley, L Malmström, B Qian, J Schonbrun, D Chivian, DE Kim, ...
Proteins: Structure, Function, and Bioinformatics 61 (S7), 128-134, 2005
1912005
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