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

Abstract


Exploring non-bonded interactions

Olga Kennard

Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, UK

brown@chemcrys.cam.ac.uk


We have used both the Cambridge Structural Database (CSD) and the Protein Databank (PDB) to investigate non-bonded interactions. The CSD currently contains approximately 160,000 entries on small-molecule crystal structures covering a wide variety of functional groups. A technique was developed to represent non-bonded interactions between selected functional groups and contact atoms in the form of 3D scattergrams or vectorgrams. These give the distribution and directionality of non-bonded contacts; often for several hundred examples, in the CSD. Comparative frequencies of interactions were also investigated. Similar information was sought from the PDB which contains about 1000 different protein-ligand structures. We have derived the chemical structures of the ligands in the form of chemical connection tables. About 300 structures with resolution equal or better than 2A were selected, and atomic positions within a radius of 4A from the ligand atoms identified. The data were transformed into Cambridge format and scattergrams and vectorgrams constructed corresponding to those obtained from the CSD. Theoretical calculations are also being carried out for comparison with the experimentally derived information. The results will become available in form of a database (IsoStar) which is likely to have widespread theoretical and practical applications.


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