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 employ and extend 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).
Publications
- Daily, M. D. & Gray, J. J. 2007 “Local motions in a benchmark of allosteric proteins,” Proteins 67(2), 385-399. (Featured cover illustration.) [4.7]
- Sivasubramanian, A., Chao, G., Pressler, H. M., Wittrup, K. D., & Gray, J. J. 2006 “Structural model of the mAb 806-EGFR complex by computational docking followed by computational and experimental mutagenesis,” Structure 14(3), 401-414. [5.5]{1}
- S. Chaudhury,* A. Sircar,* A. Sivasubramanian, M. Berrondo & J. J. Gray, "Incorporating biochemical information and backbone flexibility in RosettaDock for CAPRI rounds 6-12." Proteins, vol. 69. 4 (2007). pp. 793-800. (*These authors contributed equally to this work.)
- K. Makrodimitris, D. L. Masica, E. T. Kim & J. J. Gray. "Structure prediction of protein-solid surface interactions reveals a molecular recognition motif of statherin for hydroxyapatite." Journal of the American Chemical Society, vol. 129. 44 (2007). pp. 13713-13722.
- Gray, J. J. 2006 “Biomolecular modeling in a chemical engineering process dynamics and control course,” Chem. Eng. Ed. 40(4), 297-306.
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