In This Section      
Print This Page

Jeffrey J. Gray, Ph.D.: Key Publications

Jeffrey J. Gray, Ph.D. Jeffrey J. Gray, Ph.D.

Visit the Gray Lab >

Key Publications

Drew K, Renfrew PD, Craven T, Butterfoss GL, Chou F-C, Lyskov S, Bullock BN, Watkins A, Labonte JW, Pacella M, Kilambi KP, Leaver-Fay A, Kuhlman B, Gray JJ, Bradley P, Kirshenbaum K, Arora PS, Das R, Bonneau R. 2013. Adding Diverse Noncanonical Backbones to Rosetta: Enabling Peptidomimetic Design. Accepted for publication in PLoS One.

Xu J, Tack D, Hughes RA, Ellington AD, Gray JJ. 2013. Structure-based Non-canonical Amino Acid Design to Covalently Crosslink an Antibody-Antigen Complex. Accepted for publication in J. Struct. Biol. (Invited).

Kilambi KP, Gray JJ. 2012. Rapid Calculation of Protein pKa Values using Rosetta. Biophys. J. 103(3), 587-595.  PubMed Link

Ye Y, Stahley MR, Xu J, Friedman JI, Sun Y, McKnight JN, Gray JJ, Bowman GD, Stivers JT. 2012. Enzymatic Excision of Uracil Residues in Nucleosomes Depends on Local DNA Structure and Dynamics. Biochemistry 51(30), 6028-6038.  PubMed Link

Chaudhury S, Berrondo M, Weitzner BD, Muthu P, Bergman H, Gray JJ. 2011. Benchmarking and analysis of protein docking performance in RosettaDock 3.2. PLoS One 6(8): e22477.  PubMed Link

Berrondo M, Gray JJ. 2011. Computed structures of point deletion mutants and their enzymatic activities. Proteins 79(10), 2844-2860. (Featured cover illustration).  PubMed Link

Bocik WE, Sircar A, Gray JJ, Tolman JR. 2011. Mechanism of polyubiquitin chain recognition by the human ubiquitin conjugating enzyme Ube2g2. J. Biol. Chem. 286, 3981-3991. (co-corresponding authors).  PubMed Link

Leaver-Fay A, Tyka M, Lewis SM, Lange OF, Thompson J, Jacak R, Kaufman K, Renfrew PD, Smith CA, Sheffler W, Davis IW, Cooper S, Treuille A, Mandell DJ, Richter F, Ban YE, Fleishman SJ, Corn JE, Kim DE, Lyskov S, Berrondo M, Mentzer S, Popović Z, Havranek JJ, Karanicolas J, Das R, Meiler J, Kortemme T, Gray JJ, Kuhlman B, Baker D, Bradley P. 2011. Rosetta3: An object-oriented software suite for the simulation and design of macromolecules. Meth. Enz. 487, 545-574PubMed Link

Sircar A, Chaudhury S, Kilambi KP, Berrondo M, Gray JJ. 2010. A generalized approach to sampling backbone conformations with RosettaDock for CAPRI rounds 13-19. Proteins 78(15), 3115-3123.  PubMed Link

Berrondo M, Gray JJ, Schleif R, 2010. Computational predictions of the mutant behavior of AraC. J. Mol. Biol. 298(3), 462-470.  PubMed Link

Chaudhury S, Lyskov S, Gray JJ, 2010. PyRosetta: a script-based interface for implementing molecular modeling algorithms using Rosetta. Bioinformatics 26(5), 689-691.  PubMed Link

Chaudhury S, Gray JJ, 2009. Identification of structural mechanisms of HIV-1 protease specificity using computational peptide docking and implications for drug resistance. Structure 17(12), 1636-1648.  PubMed Link

Chaudhury S, Gray JJ, 2008. Conformer selection and induced fit in flexible backbone protein-protein docking using computational and NMR ensembles. J. Mol. Biol. 381(4), 1068-1087, PMCID: PMC2573042.  PubMed Link

Back to Top

Additional Information