Jeffrey J. Gray

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Brian KuhlmanUniversity of North CarolinaVerified email at email.unc.edu
Jeliazko R. JeliazkovGlaxoSmithKlineVerified email at gsk.com
Jason William LabonteVisiting Assistant Research Professor, Johns Hopkins UniversityVerified email at jhu.edu
Roland DunbrackFox Chase Cancer CenterVerified email at fccc.edu
Rebecca F AlfordJohnson and Johnson Innovative MedicineVerified email at its.jnj.com
Sid ChaudhuryArmed Forces Research Institute of Medical Sciences (AFRIMS), Bangkok, ThailandVerified email at health.mil
Aroop SircarSenior Scientist Immuno-Oncology, EMD Serono Research & Development Institute, Inc.Verified email at emdserono.com
Tanja KortemmeUCSFVerified email at cgl.ucsf.edu
Brian D. WeitznerOutpace BioVerified email at outpacebio.com
David BakerUniversity of WashingtonVerified email at uw.edu
David MasicaDirector of Convergence AI and Data Analytics (AbbVie)Verified email at abbvie.com
Andrew Leaver-FayResearch Assistant Professor, Biochemistry, UNCVerified email at email.unc.edu
Rhiju DasHHMI & Stanford UniversityVerified email at stanford.edu
Daisuke KurodaNational Institute of Infectious DiseasesVerified email at niid.go.jp
Krishna Praneeth KilambiHarvard Medical SchoolVerified email at mgh.harvard.edu
P. Douglas RenfrewSimons FoundationVerified email at simonsfoundation.org
Marc D. McKeeProfessor, McGill University, Montreal, Quebec, CanadaVerified email at mcgill.ca
Frank DiMaioUniversity of WashingtonVerified email at uw.edu
Matthew O'MearaUniversity of MichiganVerified email at umich.edu
Philip BradleyFred Hutchinson Cancer Research CenterVerified email at fredhutch.org

Jeffrey J. Gray

Johns Hopkins University, Chemical and Biomolecular Engineering / Program in Molecular Biophysics

Verified email at jhu.edu - Homepage

Protein-protein docking antibodies glycoproteins membrane proteins deep learning


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ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules A Leaver-Fay, M Tyka, SM Lewis, OF Lange, J Thompson, R Jacak, ... Methods in enzymology 487, 545-574, 2011	2028	2011
The Rosetta all-atom energy function for macromolecular modeling and design RF Alford, A Leaver-Fay, JR Jeliazkov, MJ O’Meara, FP DiMaio, H Park, ... Journal of chemical theory and computation 13 (6), 3031-3048, 2017	1419	2017
Protein–protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations JJ Gray, S Moughon, C Wang, O Schueler-Furman, B Kuhlman, CA Rohl, ... Journal of molecular biology 331 (1), 281-299, 2003	1359	2003
The interaction of proteins with solid surfaces JJ Gray Current opinion in structural biology 14 (1), 110-115, 2004	1049	2004
PyRosetta: a script-based interface for implementing molecular modeling algorithms using Rosetta S Chaudhury, S Lyskov, JJ Gray Bioinformatics 26 (5), 689-691, 2010	794	2010
Macromolecular modeling and design in Rosetta: recent methods and frameworks JK Leman, BD Weitzner, SM Lewis, J Adolf-Bryfogle, N Alam, RF Alford, ... Nature methods 17 (7), 665-680, 2020	678	2020
The RosettaDock server for local protein–protein docking S Lyskov, JJ Gray Nucleic acids research 36 (suppl_2), W233-W238, 2008	671	2008
Serverification of molecular modeling applications: the Rosetta Online Server that Includes Everyone (ROSIE) S Lyskov, FC Chou, SO Conchuir, BS Der, K Drew, D Kuroda, J Xu, ... PloS one 8 (5), e63906, 2013	435	2013
A comprehensive, high-resolution map of a gene’s fitness landscape E Firnberg, JW Labonte, JJ Gray, M Ostermeier Molecular biology and evolution 31 (6), 1581-1592, 2014	356	2014
Benchmarking and analysis of protein docking performance in Rosetta v3. 2 S Chaudhury, M Berrondo, BD Weitzner, P Muthu, H Bergman, JJ Gray PloS one 6 (8), e22477, 2011	344	2011
Modeling and docking of antibody structures with Rosetta BD Weitzner, JR Jeliazkov, S Lyskov, N Marze, D Kuroda, R Frick, ... Nature protocols 12 (2), 401-416, 2017	280	2017
High-resolution protein–protein docking JJ Gray Current opinion in structural biology 16 (2), 183-193, 2006	265	2006
Scientific benchmarks for guiding macromolecular energy function improvement A Leaver-Fay, MJ O'meara, M Tyka, R Jacak, Y Song, EH Kellogg, ... Methods in enzymology 523, 109-143, 2013	247	2013
Phosphorylation‐dependent inhibition of mineralization by osteopontin ASARM peptides is regulated by PHEX cleavage WN Addison, DL Masica, JJ Gray, MD McKee Journal of Bone and Mineral Research 25 (4), 695-705, 2010	240	2010
Toward high‐resolution homology modeling of antibody F_v regions and application to antibody–antigen docking A Sivasubramanian, A Sircar, S Chaudhury, JJ Gray Proteins: Structure, Function, and Bioinformatics 74 (2), 497-514, 2009	234	2009
Large-scale sequence and structural comparisons of human naive and antigen-experienced antibody repertoires BJ DeKosky, OI Lungu, D Park, EL Johnson, W Charab, C Chrysostomou, ... Proceedings of the National Academy of Sciences 113 (19), E2636-E2645, 2016	218	2016
Targeting the CoREST complex with dual histone deacetylase and demethylase inhibitors JH Kalin, M Wu, AV Gomez, Y Song, J Das, D Hayward, N Adejola, M Wu, ... Nature communications 9 (1), 53, 2018	216	2018
Deep learning in protein structural modeling and design W Gao, SP Mahajan, J Sulam, JJ Gray Patterns 1 (9), 2020	210	2020
RosettaAntibody: antibody variable region homology modeling server A Sircar, ET Kim, JJ Gray Nucleic acids research 37 (suppl_2), W474-W479, 2009	206	2009
Conformer selection and induced fit in flexible backbone protein–protein docking using computational and NMR ensembles S Chaudhury, JJ Gray Journal of molecular biology 381 (4), 1068-1087, 2008	202	2008

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