People

Research Interests

Scientific computing, primarily optimization; computational chemistry and biology, including protein and peptide structure determination, protein engineering, and drug design.

Current Research

The primary goal of Dr. Vajda's research is to develop a methodology that will permit a predictive understanding of ligand recognition by protein receptors. Such understanding is the key to rational drug and vaccine design strategies, and requires the solution of several challenging problems. The problems currently studied include (1) evaluation of binding free energy in protein-ligand complexes; (2) development of efficient docking algorithms that will find structures for the complex at or near the global free energy minimum; (3) computational solvent mapping of proteins using molecular probes - small molecules or functional groups - to identify the most favorable binding positions, (4) design of amino acid mutations to induce certain changes in the affinity and specificity of a binding site. We consider computational mapping particularly interesting, because mapping results provide detailed and reliable information on the functional sites of proteins, and hence the method is potentially very important for structural genomics and drug design applications.

Selected Recent Publications

Silberstein, M., Dennis, S., Brown III, L., Kortvelyesi, T., Clodfelter, K., Vajda, S. "Identification of substrate binding sites in enzymes by computational solvent mapping" J. Molec. Biol. 332: 1095-1113 (2003)

Prasad, J.C., Comeau, S.R., Vajda, S., Camacho, C.J. "Consensus alignment for reliable framework prediction in homology modeling" Bioinformatics 19: 1682-1691 (2003)

Kortvelyesi, T., Dennis, S., Silberstein, M., Brown III, L., Vajda, S. "Algorithms for computational solvent mapping of proteins" Proteins 51: 340-351 (2003)

Dennis S, Vajda S "Semi-global simplex optimization and its application to determining the preferred solvation sites of proteins" J. Comp. Chem. 23(3): 319-334 (2002)

Dennis S, Kortvelyesi T, Vajda S "Computational mapping identifies the binding sites of organic solvents on proteins" Proc. Natl. Acad. Sci. USA 99(7): 4290-4295 (2002)

Camacho C., Vajda S. "Protein-protein association kinetics and protein docking" Curr Opin Struct Biol 12(1): 36-40 (2002)