Search Results - Jeffrey J. Gray

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  1. 1
    The RosettaDock server for local protein-protein docking

    The RosettaDock server for local protein-protein docking by Sergey Lyskov, Jeffrey J. Gray

    Published 2008
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  2. 2
    SnugDock: Paratope Structural Optimization during Antibody-Antigen Docking Compensates for Errors in Antibody Homology Models

    SnugDock: Paratope Structural Optimization during Antibody-Antigen Docking Compensates for Errors in Antibody Homology Models by Aroop Sircar, Jeffrey J. Gray

    Published 2010
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  3. 3
    Conformer Selection and Induced Fit in Flexible Backbone Protein–Protein Docking Using Computational and NMR Ensembles

    Conformer Selection and Induced Fit in Flexible Backbone Protein–Protein Docking Using Computational and NMR Ensembles by Sidhartha Chaudhury, Jeffrey J. Gray

    Published 2008
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  4. 4
    Shape complementarity and hydrogen bond preferences in protein–protein interfaces: implications for antibody modeling and protein–protein docking

    Shape complementarity and hydrogen bond preferences in protein–protein interfaces: implications for antibody modeling and protein–protein docking by Daisuke Kuroda, Jeffrey J. Gray

    Published 2016
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  5. 5
    Pushing the Backbone in Protein-Protein Docking

    Pushing the Backbone in Protein-Protein Docking by Daisuke Kuroda, Jeffrey J. Gray

    Published 2016
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  6. 6
    Advances to tackle backbone flexibility in protein docking

    Advances to tackle backbone flexibility in protein docking by Ameya Harmalkar, Jeffrey J. Gray

    Published 2020
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  7. 7
    AI models for protein design are driving antibody engineering

    AI models for protein design are driving antibody engineering by Michael Chungyoun, Jeffrey J. Gray

    Published 2023
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  8. 8
    Allosteric Communication Occurs via Networks of Tertiary and Quaternary Motions in Proteins

    Allosteric Communication Occurs via Networks of Tertiary and Quaternary Motions in Proteins by Michael D. Daily, Jeffrey J. Gray

    Published 2009
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  9. 9
    Rapid Calculation of Protein pKa Values Using Rosetta

    Rapid Calculation of Protein pKa Values Using Rosetta by Krishna Praneeth Kilambi, Jeffrey J. Gray

    Published 2012
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  10. 10
    Fast, accurate antibody structure prediction from deep learning on massive set of natural antibodies

    Fast, accurate antibody structure prediction from deep learning on massive set of natural antibodies by Jeffrey A. Ruffolo, Jeffrey J. Gray

    Published 2022
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  11. 11
    What has AlphaFold3 learned about antibody and nanobody docking, and what remains unsolved?

    What has AlphaFold3 learned about antibody and nanobody docking, and what remains unsolved? by Fatima N. Hitawala, Jeffrey J. Gray

    Published 2024
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  12. 12
    PyRosetta: a script-based interface for implementing molecular modeling algorithms using Rosetta

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

    Published 2010
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  13. 13
    Improved prediction of antibody V<sub>L</sub>–V<sub>H</sub>orientation

    Improved prediction of antibody V<sub>L</sub>–V<sub>H</sub>orientation by Nicholas Marze, Sergey Lyskov, Jeffrey J. Gray

    Published 2016
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  14. 14
    Reliable protein-protein docking with AlphaFold, Rosetta, and replica-exchange

    Reliable protein-protein docking with AlphaFold, Rosetta, and replica-exchange by Ameya Harmalkar, Sergey Lyskov, Jeffrey J. Gray

    Published 2024
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  15. 15
    Reliable protein-protein docking with AlphaFold, Rosetta, and replica-exchange

    Reliable protein-protein docking with AlphaFold, Rosetta, and replica-exchange by Ameya Harmalkar, Sergey Lyskov, Jeffrey J. Gray

    Published 2025
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  16. 16
    RosettaAntibody: antibody variable region homology modeling server

    RosettaAntibody: antibody variable region homology modeling server by Amit Sircar, Eui Tae Kim, Jeffrey J. Gray

    Published 2009
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  17. 17
    Deciphering antibody affinity maturation with language models and weakly supervised learning

    Deciphering antibody affinity maturation with language models and weakly supervised learning by Jeffrey A. Ruffolo, Jeffrey J. Gray, Jeremias Sulam

    Published 2021
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  18. 18
    Antibody structure prediction using interpretable deep learning

    Antibody structure prediction using interpretable deep learning by Jeffrey A. Ruffolo, Jeremias Sulam, Jeffrey J. Gray

    Published 2021
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  19. 19
    FLAb: Benchmarking deep learning methods for antibody fitness prediction

    FLAb: Benchmarking deep learning methods for antibody fitness prediction by Michael Chungyoun, Jeffrey A. Ruffolo, Jeffrey J. Gray

    Published 2024
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  20. 20
    The Origin of CDR H3 Structural Diversity

    The Origin of CDR H3 Structural Diversity by Brian D. Weitzner, Roland L. Dunbrack, Jeffrey J. Gray

    Published 2015
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