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Ilya Vakser, Ph.D.
Associate Professor, Department of Applied Mathematics
and Statistics.
Funding through the National Institute of General Medicine.
Figure 1. A major challenge of post-genomic
research is to recreate the network of protein-protein 3D interactions
in living organisms |
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The research in our lab 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 building a network of connections between proteins in a genome (Fig.
1). 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. The structure-based methods
for building this network have to be fast and 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. The application
of protein recognition (docking) algorithms to inaccurate structures or
structures with conformational changes upon complex formation, at low
resolution, provides an approximate position of the proteins within the
complex. We are addressing the problem of how to transform the low-resolution
predictions to the atomic-resolution structures. We also develop a procedure
that will be capable of predicting the probability of proteins forming
a biologically relevant (or energetically stable) complex. The procedure
will rely on a number of factors, including the score/energy of the match,
a pattern of distribution of matches at different resolution (reflecting
the binding energy landscape), as well as available knowledge-based data.
An important direction in our research is development of a database of
protein-protein 3D interactions in entire genomes. It will provide the
basis for systematic studies of protein recognition and physicochemical
properties of protein association. The database will also help to identify
new drug targets and will provide the structural basis for the computer-aided
drug design.
Contact Information
email: vakser@ams.sunysb.edu
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