Department of Plant Genetics, Weizmann Institute of Science, Rehovot, ISRAEL
lpsobol@wiccmail.weizmann.ac.il
Structural databases consist of a large collection of numbers which present
atomic coordinates in three dimensional space. In some databases (for example
in PDB files) there is currently information identifying the structural
domains of proteins (subunits, helices, sheets, etc.) existing in the
retrieved information. But biologists are also interested in obtaining
information on the major interactions which stabilize the molecular structure.
We are developing software which will allow users to: 1. identify the
structural units (amino acids, cofactors or even domains) that are in surface
contact with any unit of interest and the specific interactions (including
those of charged, polar and aromatic groups) that exist between them; 2.
predict the influence of chemical modification of molecules on these
interactions (consequently on stability); 3. determine the mutual positions of
structural units (including nearest distances and angles between helicies,
beta sheets and cofactor planes).
Our approach is based on analysis of contact surface area and surface
complementarity between contacting units (1, 2).
1. Sobolev V. and Edelman M. (1995) PROTEINS, 21, 214-225.
2. Sobolev V., Wade R.C., Vriend G. and Edelman M. PROTEINS (1996), 25,
120-129.