Jeffrey J. Gray

Publication Activity (10 Years)

Years Active: 2008-2024
Publications (10 Years): 15

Top Topics

Protein Sequences

Weakly Supervised Learning

Top Venues

PLoS Comput. Biol.

Publications

Rituparna Samanta, Jeffrey J. Gray
Implicit model to capture electrostatic features of membrane environment. PLoS Comput. Biol. 20 (1) (2024)
Samuel W. Canner, Sudhanshu Shanker, Jeffrey J. Gray
Structure-based neural network protein-carbohydrate interaction predictions at the residue level. Frontiers Bioinform. 3 (2023)
Jeffrey A. Ruffolo, Jeremias Sulam, Jeffrey J. Gray
Antibody structure prediction using interpretable deep learning. Patterns 3 (2) (2022)
Ameya Harmalkar, Sai Pooja Mahajan, Jeffrey J. Gray
Induced fit with replica exchange improves protein complex structure prediction. PLoS Comput. Biol. 18 (6) (2022)
Jeffrey A. Ruffolo, Jeffrey J. Gray, Jeremias Sulam
Deciphering antibody affinity maturation with language models and weakly supervised learning. CoRR (2021)
Julia Koehler Leman, Brian D. Weitzner, P. Douglas Renfrew, Steven M. Lewis, Rocco Moretti, Andrew M. Watkins, Vikram Khipple Mulligan, Sergey Lyskov, Jared Adolf-Bryfogle, Jason W. Labonte, Justyna Krys, RosettaCommons Consortium, Christopher Bystroff, William R. Schief, Dominik Gront, Ora Schueler-Furman, David Baker, Philip Bradley, Roland L. Dunbrack Jr., Tanja Kortemme, Andrew Leaver-Fay, Charlie E. M. Strauss, Jens Meiler, Brian Kuhlman, Jeffrey J. Gray, Richard Bonneau
Better together: Elements of successful scientific software development in a distributed collaborative community. PLoS Comput. Biol. 16 (5) (2020)
Wenhao Gao, Sai Pooja Mahajan, Jeremias Sulam, Jeffrey J. Gray
Deep Learning in Protein Structural Modeling and Design. CoRR (2020)
Jeffrey A. Ruffolo, Carlos Guerra, Sai Pooja Mahajan, Jeremias Sulam, Jeffrey J. Gray
Geometric potentials from deep learning improve prediction of CDR H3 loop structures. Bioinform. 36 (Supplement-1) (2020)
Wenhao Gao, Sai Pooja Mahajan, Jeremias Sulam, Jeffrey J. Gray
Deep Learning in Protein Structural Modeling and Design. Patterns 1 (9) (2020)
Nicholas A. Marze, Shourya S. Roy Burman, William Sheffler, Jeffrey J. Gray
Efficient flexible backbone protein-protein docking for challenging targets. Bioinform. 34 (20) (2018)
Julia Koehler Leman, Benjamin K. Mueller, Jeffrey J. Gray
Expanding the toolkit for membrane protein modeling in Rosetta. Bioinform. 33 (5) (2017)
Jason W. Labonte, Jared Adolf-Bryfogle, William R. Schief, Jeffrey J. Gray
Residue-centric modeling and design of saccharide and glycoconjugate structures. J. Comput. Chem. 38 (5) (2017)
Rebecca F. Alford, Andrew Leaver-Fay, Lynda Gonzales, Erin L. Dolan, Jeffrey J. Gray
A cyber-linked undergraduate research experience in computational biomolecular structure prediction and design. PLoS Comput. Biol. 13 (12) (2017)
Daisuke Kuroda, Jeffrey J. Gray
Shape complementarity and hydrogen bond preferences in protein-protein interfaces: implications for antibody modeling and protein-protein docking. Bioinform. 32 (16) (2016)
Rebecca F. Alford, Julia Koehler Leman, Brian D. Weitzner, Amanda M. Duran, Drew C. Tilley, Assaf Elazar, Jeffrey J. Gray
An Integrated Framework Advancing Membrane Protein Modeling and Design. PLoS Comput. Biol. 11 (9) (2015)
Krishna Praneeth Kilambi, Kavan Reddy, Jeffrey J. Gray
Protein-Protein Docking with Dynamic Residue Protonation States. PLoS Comput. Biol. 10 (12) (2014)
Sidhartha Chaudhury, Sergey Lyskov, Jeffrey J. Gray
PyRosetta: a script-based interface for implementing molecular modeling algorithms using Rosetta. Bioinform. 26 (5) (2010)
Aroop Sircar, Jeffrey J. Gray
SnugDock: Paratope Structural Optimization during Antibody-Antigen Docking Compensates for Errors in Antibody Homology Models. PLoS Comput. Biol. 6 (1) (2010)
Michael D. Daily, Jeffrey J. Gray
Allosteric Communication Occurs via Networks of Tertiary and Quaternary Motions in Proteins. PLoS Comput. Biol. 5 (2) (2009)
Aroop Sircar, Eric T. Kim, Jeffrey J. Gray
RosettaAntibody: antibody variable region homology modeling server. Nucleic Acids Res. 37 (Web-Server-Issue) (2009)
Sergey Lyskov, Jeffrey J. Gray
The RosettaDock server for local protein-protein docking. Nucleic Acids Res. 36 (Web-Server-Issue) (2008)