Vakser Lab

The research in our laboratory focuses on molecular modeling in the context of structural genomics and bioinformatics. The major goals are to develop approaches to the modeling of protein interactions and to design procedures for reconstruction of the network of connections between proteins in a genome. The number of protein-protein interactions in a genome is significantly larger than the number of individual proteins. Moreover, most protein structures will be models of limited accuracy. Thus the structure-based methods for building this network have to be (a) fast, and (b) insensitive to significant inaccuracies of modeled structures. The precision of these methods may be correlated with the precision of the protein structures – lower for less accurate models and higher for more exact models.

Our long-term goals are to understand the fundamental principles of protein interaction and to create a structure-based description of genomes. The primary current objectives are: development of methodology for an accurate prediction of the structure of protein complexes, docking in genome-wide databases of modeled protein structures, and development of the integrated environment for docking studies.

Representative Publications

• Katchalski-Katzir, E., Shariv, I., Eisenstein, M., Friesem, A.A., Aflalo, C., Vakser, I.A., 1992, Molecular surface recognition: Determination of geometric fit between proteins and their ligands by correlation techniques, Proc. Natl. Acad. Sci. USA, 89:2195-2199
• Vakser, I.A., Aflalo, C., 1994, Hydrophobic docking: A proposed enhancement to molecular recognition techniques, Proteins, 20:320-329
• Vakser, I.A., 1995, Protein docking for low-resolution structures, Protein Eng., 8:371-377.
• Vakser, I.A., 1996, Long-distance potentials: An approach to the multiple-minima problem in ligand-receptor interaction, Protein Eng., 9:37-41.
• Vakser, I.A., Matar, O.G., Lam, C.F., 1999, A systematic study of low-resolution recognition in protein-protein complexes, Proc. Natl. Acad. Sci. USA, 96:8477-8482.
• Tovchigrechko, A., Vakser, I.A., 2001, How common is the funnel-like energy landscape in protein-protein interactions? Protein Sci., 10:1572-1583.
• Vajda, S., Vakser, I.A., Sternberg, M.J.E., Janin, J., 2002, Modeling of protein interactions in genomes, Proteins, 47: 444-446.
• Tovchigrechko, A., Wells, C.A., Vakser, I.A., 2002, Docking of protein models, Protein Sci., 11:1888-1896.
• Janin, J., Henrick, K., Moult, J., Ten Eyck, L.F., Sternberg, M.J.E., Vajda, S., Vakser, I.A., Wodak, S.J. 2003, CAPRI: A Critical Assessment of PRedicted Interactions, Proteins, 52:2-9.
• Jiang, S., Tovchigrechko, A., Vakser, I.A., 2003, The role of geometric complementarity in secondary structure packing: A systematic docking study, Protein Sci., 12:1646-1651.
• Jiang, S., Vakser, I.A., 2004, Shorter side chains optimize helix-helix packing, Protein Sci., 13:1426-1429.
• Vakser, I.A., 2004, Protein-protein interfaces are special, Structure, 12:910-912.