Matching of PDB chain sequences to information in public databases as a prerequisite for 3D functional site visualization
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doi:10.2390/biecoll-jib-2004-7
June 25, 2004
October 14, 2004
Guido Dieterich, Dirk W. Heinz, and Joachim Reichelt
Correspondence should be addressed to:
Guido Dieterich
GBF, SB, Mascheroder Weg 1, 38124 Braunschweig, D-Germany
ed.fbg@nullhcireteid.odiug
Abstract
The 3D structures of biomacromolecules stored in the Protein Data Bank were correlated with different external, biological information from public databases. We have matched the feature table of SWISS-PROT entries and a local version of InterProScan with the corresponding 3D-structures. OMIM (Online Mendelian Inheritance in Man) records, containing information of genetic disorders, were extracted and linked to the structures. The exhaustive all-against-all 3D structure comparison of protein structures stored in DALI was condensed into in single files for each PDB entry. Results are stored in XML format facilitating its incorporation into related software. The resulting annotation of the protein structures allows functional sites to be readily identified upon visualization.