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Jeffrey J. Gray
Jeffrey J. Gray
Johns Hopkins University, Chemical and Biomolecular Engineering / Program in Molecular Biophysics
Verified email at jhu.edu - Homepage
Title
Cited by
Cited by
Year
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
19312011
Protein–protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations
JJ Gray, S Moughon, C Wang, O Schueler-Furman, B Kuhlman, CA Rohl, ...
Journal of molecular biology 331 (1), 281-299, 2003
13062003
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
12372017
The interaction of proteins with solid surfaces
JJ Gray
Current opinion in structural biology 14 (1), 110-115, 2004
10362004
PyRosetta: a script-based interface for implementing molecular modeling algorithms using Rosetta
S Chaudhury, S Lyskov, JJ Gray
Bioinformatics 26 (5), 689-691, 2010
7172010
The RosettaDock server for local protein–protein docking
S Lyskov, JJ Gray
Nucleic acids research 36 (suppl_2), W233-W238, 2008
6372008
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
5582020
Serverification of molecular modeling applications: the Rosetta Online Server that Includes Everyone (ROSIE)
S Lyskov, FC Chou, SO Conchuir, BS Der, K Drew, D Kuroda, J Xu, ...
PloS one 8 (5), e63906, 2013
3942013
A comprehensive, high-resolution map of a gene’s fitness landscape
E Firnberg, JW Labonte, JJ Gray, M Ostermeier
Molecular biology and evolution 31 (6), 1581-1592, 2014
3302014
Benchmarking and analysis of protein docking performance in Rosetta v3. 2
S Chaudhury, M Berrondo, BD Weitzner, P Muthu, H Bergman, JJ Gray
PloS one 6 (8), e22477, 2011
3272011
Modeling and docking of antibody structures with Rosetta
BD Weitzner, JR Jeliazkov, S Lyskov, N Marze, D Kuroda, R Frick, ...
Nature protocols 12 (2), 401-416, 2017
2622017
High-resolution protein–protein docking
JJ Gray
Current opinion in structural biology 16 (2), 183-193, 2006
2592006
Scientific benchmarks for guiding macromolecular energy function improvement
A Leaver-Fay, MJ O'Meara, M Tyka, R Jacak, Y Song, EH Kellogg, ...
Methods in enzymology 523, 109-143, 2013
2442013
Phosphorylation‐dependent inhibition of mineralization by osteopontin ASARM peptides is regulated by PHEX cleavage
WN Addison, DL Masica, JJ Gray, MD McKee
Journal of Bone and Mineral Research 25 (4), 695-705, 2010
2352010
Toward high‐resolution homology modeling of antibody Fv regions and application to antibody–antigen docking
A Sivasubramanian, A Sircar, S Chaudhury, JJ Gray
Proteins: Structure, Function, and Bioinformatics 74 (2), 497-514, 2009
2262009
Large-scale sequence and structural comparisons of human naive and antigen-experienced antibody repertoires
BJ DeKosky, OI Lungu, D Park, EL Johnson, W Charab, C Chrysostomou, ...
Proceedings of the National Academy of Sciences 113 (19), E2636-E2645, 2016
2022016
RosettaAntibody: antibody variable region homology modeling server
A Sircar, ET Kim, JJ Gray
Nucleic acids research 37 (suppl_2), W474-W479, 2009
1982009
Targeting the CoREST complex with dual histone deacetylase and demethylase inhibitors
JH Kalin, M Wu, AV Gomez, Y Song, J Das, D Hayward, N Adejola, M Wu, ...
Nature communications 9 (1), 53, 2018
1942018
Conformer selection and induced fit in flexible backbone protein–protein docking using computational and NMR ensembles
S Chaudhury, JJ Gray
Journal of molecular biology 381 (4), 1068-1087, 2008
1942008
Deep learning in protein structural modeling and design
W Gao, SP Mahajan, J Sulam, JJ Gray
Patterns 1 (9), 2020
1772020
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Articles 1–20