Jeffrey Gray

Assistant Professor

Office:  (410) 516-5313
Email: jgray@jhu.edu
Curriculum Vitae

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

• Chaudhury, S. & Gray, J. J. 2008 “Conformer selection and induced fit in flexible backbone protein-protein docking using computational and NMR ensembles,” Journal of Molecular Biology 381(4), 1068-1087. 
• Berrondo, M., Ostermeier, M. & Gray, J. J. 2008 “Structure prediction of domain insert proteins from structures of individual domains,” Structure 16(4), 513-527. 
• Daily, M. D., Upadhyaya, T. & J. J. Gray, 2008 “Contact rearrangements form coupled networks from local motions in allosteric proteins,” Proteins 71(4), 455-466. 
• K. Makrodimitris, D. L. Masica, E. T. Kim & J. J. Gray, 2007 “Structure prediction of protein-solid surface interactions reveals a molecular recognition motif of statherin for hydroxyapatite,” Journal of the  American Chemical Society 129(44), 13713-13722.
• Gray, J. J. 2006 “High-resolution protein-protein docking,” Current Opinion in Structural Biology 40(4), 183-193.