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Bioinformatics Vol. 16 no. 4 2000
Pages 372-375
© 2000 Oxford University Press

Database of Structural Motifs in Proteins

Kunchur Guruprasad 1, Maheshuni S. Prasad 1 and Gundu R. Kumar 1

1 Centre for DNA Fingerprinting and Diagnostics (CDFD), Nacharam, Hyderabad - 500 076, India

Received on September 29, 1999 ; revised on November 15, 1999 ; accepted on November 15, 1999

Summary: The database of structural motifs in proteins (DSMP) contains data relevant to helices, ß-turns, {gamma}-turns, ß-hairpins, {psi}-loops, ß-{alpha}-ß motifs, ß-sheets, ß-strands and disulphide bridges extracted from all proteins in the Protein Data Bank primarily using the PROMOTIF program and implemented as a web-based network service using the SRS. The data corresponding to the structural motifs includes; sequence, position in polypeptide chain, geometry, type, unique code, keywords and resolution of crystal structure. This data is available for a representative data set of 1028 protein chains and also for all 10 213 proteins in the Protein Data Bank. The three-dimensional coordinates for all structural motifs (except sheet and disulphide bridge) are also available for the representative data set. Using features in SRS, DSMP can be queried to extract information from one or more structural motifs that may be useful for sequence-structure analysis, prediction, modelling or design.

Availability: http://www.cdfd.org.in/dsmp.html

Contact: guru{at}www.cdfd.org.in


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