Education
- Post-Doctoral, Biochemistry. University of
Washington. 2002
- Ph.D., Chemical Engineering. University of Texas at
Austin. 2000
- B.S.E., Chemical Engineering. University of Michigan,
Ann Arbor. 1994
Research Interests
We create and apply protein structure prediction methods
to
address practical problems in biomolecular self-assembly and function.
Recent problems we have studied include protein-protein docking
(developing new techniques in Monte Carlo minimization, ensemble
docking, and pH-dependent side-chain packing), therapeutic antibodies
(integrating knowledge-based homology modeling and high-resolution loop
modeling, flexible loop docking, computational mutagenesis), proteins
interacting with solid surfaces (Monte Carlo minimization,
protein-surface energy functions, post-translationally modified amino
acids, protein design), and allostery (contact rearrangment networks,
rigid-body motion networks).
Selected Publications
- S. Chaudhury, S. Lyskov & J. J. Gray, "PyRosetta:
a
script-based interface for implementing molecular modeling algorithms
using Rosetta," Bioinformatics, 26(5), 689-691 (2010).
- A. Sircar & J. J. Gray, "SnugDock:
Paratope structural optimization during antibody-antigen docking
compensates for errors in antibody homology models," PLoS
Comput. Biol. 6(1): e1000644 (2010).
- S. Chaudhury & J. J. Gray, "Identification
of structural mechanisms of HIV-1 protease specificity using
computational peptide docking and implications for drug resistance,"
Structure 17(12), 1636-1648 (2009).
- A. Sircar,* E. Kim* & J. J. Gray, “RosettaAntibody:
Antibody Variable Region Homology Modeling Server,”
Nucleic Acids Research 37 (Web Server Issue), W474-W479 (2009).
[*These authors contributed equally to this work]
- D. L. Masica & J. J. Gray, “Solution-
and adsorbed-state structural ensembles predicted for the
statherin-hydroxyapatite system,” Biophys. J.
96(8), 3082-3091 (2009).
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