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Nucleic Acids Research 2006 34(Database Issue):D285-D286; doi:10.1093/nar/gkj125
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Nucleic Acids Research, 2006, Vol. 34, Database issue D285-D286
© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oxfordjournals.org

Article

iMOTdb—a comprehensive collection of spatially interacting motifs in proteins

Ganesan Pugalenthi, Anirban Bhaduri and R. Sowdhamini*

National Centre for Biological Sciences, Tata Institute of Fundamental Research UAS-GKVK Campus, Bellary Road, Bangalore 560 065, India

*To whom correspondence should be addressed. Tel: +91 80 23636421; Fax: +91 80 23636462; Email: mini{at}ncbs.res.in

Received August 15, 2005. Accepted October 21, 2005.

Realization of conserved residues that represent a protein family is crucial for clearer understanding of biological function as well as for the better recognition of additional members in sequence databases. Functionally important residues are recognized well due to their high degree of conservation in closely related sequences and are annotated in functional motif databases. Structural motifs are central to the integrity of the fold and require careful analysis for their identification. We report the availability of a database of spatially interacting motifs in single protein structures as well as those among distantly related protein structures that belong to a superfamily. Spatial interactions amongst conserved motifs are automatically measured using sequence similarity scores and distance calculations. Interactions between pairs of conserved motifs are described in the form of pseudoenergies. iMOTdb database provides information for 854 488 motifs corresponding to 60 849 protein structural domains and 22 648 protein structural entries.

Present address: Anirban Bhaduri, Information and Mathematical Sciences, Genome Institute of Singapore, Genome, 60 Biopolis Street, Singapore


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