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ORCIDJeffrey J. Gray
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2020 – today
- 2024
[j20]Rituparna Samanta
, Jeffrey J. Gray:
Implicit model to capture electrostatic features of membrane environment. PLoS Comput. Biol. 20(1) (2024)- [j19]Jared Adolf-Bryfogle, Jason W. Labonte, John C. Kraft, Maxim Shapovalov, Sebastian Raemisch, Thomas Lütteke, Frank Dimaio, Christopher D. Bahl, Jesper Pallesen, Neil P. King, Jeffrey J. Gray, Daniel W. Kulp, William R. Schief:
Growing Glycans in Rosetta: Accurate de novo glycan modeling, density fitting, and rational sequon design. PLoS Comput. Biol. 20(6): 1011895 (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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