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Jeffrey J. Gray
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2020 – today
- 2024
- [j19]Rituparna Samanta
, Jeffrey J. Gray
:
Implicit model to capture electrostatic features of membrane environment. PLoS Comput. Biol. 20(1) (2024) - 2023
- [j18]Samuel W. Canner, Sudhanshu Shanker, Jeffrey J. Gray:
Structure-based neural network protein-carbohydrate interaction predictions at the residue level. Frontiers Bioinform. 3 (2023) - 2022
- [j17]Jeffrey A. Ruffolo
, Jeremias Sulam, Jeffrey J. Gray
:
Antibody structure prediction using interpretable deep learning. Patterns 3(2): 100406 (2022) - [j16]Ameya Harmalkar
, Sai Pooja Mahajan
, Jeffrey J. Gray
:
Induced fit with replica exchange improves protein complex structure prediction. PLoS Comput. Biol. 18(6) (2022) - 2021
- [i2]Jeffrey A. Ruffolo, Jeffrey J. Gray, Jeremias Sulam:
Deciphering antibody affinity maturation with language models and weakly supervised learning. CoRR abs/2112.07782 (2021) - 2020
- [j15]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): i268-i275 (2020) - [j14]Wenhao Gao
, Sai Pooja Mahajan
, Jeremias Sulam
, Jeffrey J. Gray
:
Deep Learning in Protein Structural Modeling and Design. Patterns 1(9): 100142 (2020) - [j13]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) - [i1]Wenhao Gao
, Sai Pooja Mahajan, Jeremias Sulam, Jeffrey J. Gray:
Deep Learning in Protein Structural Modeling and Design. CoRR abs/2007.08383 (2020)
2010 – 2019
- 2018
- [j12]Nicholas A. Marze, Shourya S. Roy Burman
, William Sheffler, Jeffrey J. Gray
:
Efficient flexible backbone protein-protein docking for challenging targets. Bioinform. 34(20): 3461-3469 (2018) - 2017
- [j11]Julia Koehler Leman, Benjamin K. Mueller, Jeffrey J. Gray
:
Expanding the toolkit for membrane protein modeling in Rosetta. Bioinform. 33(5): 754-756 (2017) - [j10]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): 276-287 (2017) - [j9]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) - 2016
- [j8]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): 2451-2456 (2016) - 2015
- [j7]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) - 2014
- [j6]Krishna Praneeth Kilambi
, Kavan Reddy, Jeffrey J. Gray
:
Protein-Protein Docking with Dynamic Residue Protonation States. PLoS Comput. Biol. 10(12) (2014) - 2010
- [j5]Sidhartha Chaudhury, Sergey Lyskov, Jeffrey J. Gray
:
PyRosetta: a script-based interface for implementing molecular modeling algorithms using Rosetta. Bioinform. 26(5): 689-691 (2010) - [j4]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)
2000 – 2009
- 2009
- [j3]Aroop Sircar, Eric T. Kim, Jeffrey J. Gray
:
RosettaAntibody: antibody variable region homology modeling server. Nucleic Acids Res. 37(Web-Server-Issue): 474-479 (2009) - [j2]Michael D. Daily, Jeffrey J. Gray
:
Allosteric Communication Occurs via Networks of Tertiary and Quaternary Motions in Proteins. PLoS Comput. Biol. 5(2) (2009) - 2008
- [j1]Sergey Lyskov, Jeffrey J. Gray
:
The RosettaDock server for local protein-protein docking. Nucleic Acids Res. 36(Web-Server-Issue): 233-238 (2008)
Coauthor Index
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last updated on 2024-08-05 21:15 CEST by the dblp team
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