World's Best Scientists 2026 revealed!

D-Index & Metrics

Biology and Biochemistry

D-Index
66
Citations
20179
World Ranking
8513
National Ranking
3829

Research.com Recognitions

  • 2016 - Fellow of the Indian National Academy of Engineering (INAE)

Overview

Jeffrey J. Gray is affiliated with Johns Hopkins University in the United States. Their research primarily focuses on the fields of biochemistry, genetics, and molecular biology, with particular contributions to molecular biology, radiology, nuclear medicine and imaging, materials chemistry, immunology, and computational theory and mathematics.

The scientist's work spans several main topics, including monoclonal and polyclonal antibodies research, glycosylation and glycoproteins research, protein structure and dynamics, RNA and protein synthesis mechanisms, enzyme structure and function, protein purification and stability, and computational drug discovery methods.

Recent publications by Jeffrey J. Gray include:

  • Macromolecular modeling and design in Rosetta: recent methods and frameworks, 2020, Nature Methods
  • Fast, accurate antibody structure prediction from deep learning on massive set of natural antibodies, 2023, Nature Communications
  • Deep Learning in Protein Structural Modeling and Design, 2020, Patterns
  • Antibody structure prediction using interpretable deep learning, 2021, Patterns
  • Rosetta3: An Object-Oriented Software Suite for the Simulation and Design of Macromolecules, 2020, UNC Libraries

Their collaborative network includes frequent co-authors such as Jeffrey A. Ruffolo, Jason W. Labonte, Sai Pooja Mahajan, Sergey Lyskov, and Brian Kuhlman.

Jeffrey J. Gray's publications have often appeared in venues including bioRxiv (Cold Spring Harbor Laboratory), Biophysical Journal, UNC Libraries, Zenodo (CERN European Organization for Nuclear Research), and OPAL (Open@LaTrobe) (La Trobe University).

In recognition of their contributions, Jeffrey J. Gray was named Fellow of the Indian National Academy of Engineering (INAE) in 2016.

Best Publications

  • ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules.

    Andrew Leaver-Fay;Michael Tyka;Steven M. Lewis;Oliver F. Lange

  • Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations.

    Jeffrey J. Gray;Stewart Moughon;Chu Wang;Ora Schueler-Furman

  • The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design.

    Rebecca F. Alford;Andrew Leaver-Fay;Jeliazko R. Jeliazkov;Matthew J. O’Meara

  • The interaction of proteins with solid surfaces.

    Jeffrey J Gray

  • Macromolecular modeling and design in Rosetta: recent methods and frameworks

    Julia Koehler Leman;Brian D. Weitzner;Brian D. Weitzner;Steven M. Lewis;Steven M. Lewis;Jared Adolf-Bryfogle

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

    Sidhartha Chaudhury;Sergey Lyskov;Jeffrey J. Gray

  • The RosettaDock server for local protein–protein docking

    Sergey Lyskov;Jeffrey J. Gray

  • Serverification of molecular modeling applications: the Rosetta Online Server that Includes Everyone (ROSIE).

    Sergey Lyskov;Fang Chieh Chou;Shane Ó Conchúir;Bryan S. Der

  • A comprehensive, high-resolution map of a gene's fitness landscape

    Elad Firnberg;Jason W. Labonte;Jeffrey J. Gray;Marc Ostermeier

  • Benchmarking and analysis of protein docking performance in Rosetta v3.2.

    Sidhartha Chaudhury;Monica Berrondo;Brian D. Weitzner;Pravin Muthu

  • Modeling and docking of antibody structures with Rosetta

    Brian D Weitzner;Jeliazko R Jeliazkov;Sergey Lyskov;Nicholas Marze

  • High-resolution protein–protein docking

    Jeffrey J Gray

  • Scientific Benchmarks for Guiding Macromolecular Energy Function Improvement

    Andrew P Leaver-Fay;Matthew J. O'Meara;Mike Tyka;Ron Jacak

  • Toward high-resolution homology modeling of antibody Fv regions and application to antibody-antigen docking.

    Arvind Sivasubramanian;Aroop Sircar;Sidhartha Chaudhury;Jeffrey J. Gray

  • Phosphorylation-dependent inhibition of mineralization by osteopontin ASARM peptides is regulated by PHEX cleavage

    William N Addison;David L Masica;Jeffrey J Gray;Marc D McKee

  • Targeting the CoREST complex with dual histone deacetylase and demethylase inhibitors

    Jay H. Kalin;Jay H. Kalin;Muzhou Wu;Andrea V. Gomez;Yun Song

  • Conformer selection and induced fit in flexible backbone protein-protein docking using computational and NMR ensembles

    Sidhartha Chaudhury;Jeffrey J. Gray

  • RosettaAntibody: antibody variable region homology modeling server

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

  • Large-scale sequence and structural comparisons of human naive and antigen-experienced antibody repertoires

    Brandon J. DeKosky;Oana I. Lungu;Daechan Park;Erik L. Johnson

  • SnugDock: paratope structural optimization during antibody-antigen docking compensates for errors in antibody homology models.

    Aroop Sircar;Jeffrey J. Gray

Frequent Co-Authors

Brian Kuhlman
Brian Kuhlman University of North Carolina at Chapel Hill
David Baker
David Baker University of Washington
Tanja Kortemme
Tanja Kortemme University of California, San Francisco
Richard Bonneau
Richard Bonneau New York University
Roland L. Dunbrack
Roland L. Dunbrack Fox Chase Cancer Center
William R. Schief
William R. Schief Scripps Research Institute
Jens Meiler
Jens Meiler Vanderbilt University
Rhiju Das
Rhiju Das Stanford University
Marc D. McKee
Marc D. McKee McGill University
Brian G. Pierce
Brian G. Pierce University of Maryland, College Park

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