The RosettaDock server for local protein-protein docking. - Sergey Lyskov; Jeffrey J. Gray (Nucleic Acids Res., 2008)

RosettaAntibody: antibody variable region homology modeling server. - Aroop Sircar; Eric T. Kim; Jeffrey J. Gray (Nucleic Acids Res., 2009)

Allosteric Communication Occurs via Networks of Tertiary and Quaternary Motions in Proteins. - Michael D. Daily; Jeffrey J. Gray (PLoS Comput. Biol., 2009)

PyRosetta: a script-based interface for implementing molecular modeling algorithms using Rosetta. - Sidhartha Chaudhury; Sergey Lyskov; Jeffrey J. Gray (Bioinform., 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)

Protein-Protein Docking with Dynamic Residue Protonation States. - Krishna Praneeth Kilambi; Kavan Reddy; Jeffrey J. Gray (PLoS Comput. Biol., 2014)

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)

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)

Expanding the toolkit for membrane protein modeling in Rosetta. - Julia Koehler Leman; Benjamin K. Mueller; Jeffrey J. Gray (Bioinform., 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)

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)

Efficient flexible backbone protein-protein docking for challenging targets. - Nicholas A. Marze; Shourya S. Roy Burman; William Sheffler; Jeffrey J. Gray (Bioinform., 2018)

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)

Deep Learning in Protein Structural Modeling and Design. - Wenhao Gao 001; Sai Pooja Mahajan; Jeremias Sulam; Jeffrey J. Gray (Patterns, 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; et al. (PLoS Comput. Biol., 2020)

Deciphering antibody affinity maturation with language models and weakly supervised learning. - Jeffrey A. Ruffolo; Jeffrey J. Gray; Jeremias Sulam (CoRR, 2021)

Antibody structure prediction using interpretable deep learning. - Jeffrey A. Ruffolo; Jeremias Sulam; Jeffrey J. Gray (Patterns, 2022)

Induced fit with replica exchange improves protein complex structure prediction. - Ameya Harmalkar; Sai Pooja Mahajan; Jeffrey J. Gray (PLoS Comput. Biol., 2022)

Structure-based neural network protein-carbohydrate interaction predictions at the residue level. - Samuel W. Canner; Sudhanshu Shanker; Jeffrey J. Gray (Frontiers Bioinform., 2023)

Growing Glycans in Rosetta: Accurate de novo glycan modeling, density fitting, and rational sequon design. - 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; et al. (PLoS Comput. Biol., 2024)

Implicit model to capture electrostatic features of membrane environment. - Rituparna Samanta; Jeffrey J. Gray (PLoS Comput. Biol., 2024)