Jeffrey J. Gray

According to our database, Jeffrey J. Gray authored at least 20 papers between 2008 and 2024.

Collaborative distances:

• Dijkstra number of five.
• Erdős number of four.

2024

Implicit model to capture electrostatic features of membrane environment.

Rituparna Samanta, Jeffrey J. Gray

PLoS Comput. Biol., January, 2024

2023

Structure-based neural network protein-carbohydrate interaction predictions at the residue level.

Samuel W. Canner, Sudhanshu Shanker, Jeffrey J. Gray

Frontiers Bioinform., May, 2023

2022

Induced fit with replica exchange improves protein complex structure prediction.

Ameya Harmalkar, Sai Pooja Mahajan, Jeffrey J. Gray

PLoS Comput. Biol., 2022

Antibody structure prediction using interpretable deep learning.

Jeffrey A. Ruffolo, Jeremias Sulam, Jeffrey J. Gray

Patterns, 2022

2021

Deciphering antibody affinity maturation with language models and weakly supervised learning.

Jeffrey A. Ruffolo, Jeffrey J. Gray, Jeremias Sulam

CoRR, 2021

2020

Better together: Elements of successful scientific software development in a distributed collaborative community.

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

PLoS Comput. Biol., 2020

Deep Learning in Protein Structural Modeling and Design.

Wenhao Gao, Sai Pooja Mahajan, Jeremias Sulam, Jeffrey J. Gray

Patterns, 2020

Geometric potentials from deep learning improve prediction of CDR H3 loop structures.

Jeffrey A. Ruffolo, Carlos Guerra, Sai Pooja Mahajan, Jeremias Sulam, Jeffrey J. Gray

Bioinform., 2020

2018

Efficient flexible backbone protein-protein docking for challenging targets.

Nicholas A. Marze, Shourya S. Roy Burman, William Sheffler, Jeffrey J. Gray

Bioinform., 2018

2017

A cyber-linked undergraduate research experience in computational biomolecular structure prediction and design.

Rebecca F. Alford, Andrew Leaver-Fay, Lynda Gonzales, Erin L. Dolan, Jeffrey J. Gray

PLoS Comput. Biol., 2017

Residue-centric modeling and design of saccharide and glycoconjugate structures.

Jason W. Labonte, Jared Adolf-Bryfogle, William R. Schief, Jeffrey J. Gray

J. Comput. Chem., 2017

Expanding the toolkit for membrane protein modeling in Rosetta.

Julia Koehler Leman, Benjamin K. Mueller, Jeffrey J. Gray

Bioinform., 2017

2016

Shape complementarity and hydrogen bond preferences in protein-protein interfaces: implications for antibody modeling and protein-protein docking.

Daisuke Kuroda, Jeffrey J. Gray

Bioinform., 2016

2015

An Integrated Framework Advancing Membrane Protein Modeling and Design.

Rebecca F. Alford, Julia Koehler Leman, Brian D. Weitzner, Amanda M. Duran, Drew C. Tilley, Assaf Elazar, Jeffrey J. Gray

PLoS Comput. Biol., 2015

2014

Protein-Protein Docking with Dynamic Residue Protonation States.

Krishna Praneeth Kilambi, Kavan Reddy, Jeffrey J. Gray

PLoS Comput. Biol., 2014

2010

SnugDock: Paratope Structural Optimization during Antibody-Antigen Docking Compensates for Errors in Antibody Homology Models.

Aroop Sircar, Jeffrey J. Gray

PLoS Comput. Biol., 2010

PyRosetta: a script-based interface for implementing molecular modeling algorithms using Rosetta.

Sidhartha Chaudhury, Sergey Lyskov, Jeffrey J. Gray

Bioinform., 2010

2009

Allosteric Communication Occurs via Networks of Tertiary and Quaternary Motions in Proteins.

Michael D. Daily, Jeffrey J. Gray

PLoS Comput. Biol., 2009

RosettaAntibody: antibody variable region homology modeling server.

Aroop Sircar, Eric T. Kim, Jeffrey J. Gray

Nucleic Acids Res., 2009

2008

The RosettaDock server for local protein-protein docking.

Sergey Lyskov, Jeffrey J. Gray

Nucleic Acids Res., 2008