Ilya Vakser

Ilya Vakser
  • Director
  • Professor


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.

Selected 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., 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., Wells, C.A., Vakser, I.A., 2002, Docking of protein models, Protein Sci., 11:1888-1896.
  • Gao, Y., Douguet, D., Tovchigrechko, A., Vakser, I.A., 2007, Dockground system of databases for protein recognition studies: Unbound structures for docking, Proteins, 69:845-851.
  • Hunjan, J., Tovchigrechko, A., Gao, Y., Vakser, I.A., 2008, The size of the intermolecular energy funnel in protein-protein interactions, Proteins, 72:344–352.
  • Ruvinsky, A.M., Vakser, I.A., 2008, Chasing funnels on protein-protein energy landscapes at different resolutions, Biophys. J., 95:2150–2159.
  • Kundrotas, P.J., Zhu, Z., Vakser, I.A., 2010, GWIDD: Genome-Wide Protein Docking Database, Nucl. Acids Res., 38:D513-517.
  • Kundrotas, P.J., Vakser, I.A., 2010, Accuracy of protein-protein binding sites in high-throughput template-based modeling, PLoS Comp. Biol., 6: e1000727.
  • Ruvinsky, A.M., Kirys, T., Tuzikov, A.V., Vakser, I.A., 2011, Side-chain conformational changes upon protein-protein association, J. Mol. Biol., 408: 356–365.
  • Kundrotas, P.J., Zhu, Z., Janin, J., Vakser, I.A., 2012, Templates are available to model nearly all complexes of structurally characterized proteins, Proc. Natl. Acad. Sci. USA, 109: 9438–9441