BIOINFORMATICS<-->STRUCTURE
Jerusalem, Israel, November 17-21, 1996

Abstract


Computational tools for analysis of structural data in the PDB

Vladimir Sobolev and Marvin Edelman

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.


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