iMOT: An interactive package for the selection of spatially interacting motifs

A. Bhaduri, Pugalenthi Ganesan, N. Gupta, R. Sowdhamini*

*Corresponding author for this work

    Research output: Contribution to journalArticlepeer-review

    9 Scopus citations

    Abstract

    Functional selection and three-dimensional structural constraints of proteins relate to the retention of significant sequence similarity between proteins of similar fold and function despite poor overall sequence identity and evolutionary pressures. We report the availability of 'iMOT' (interacting MOTif) server, an interactive package for the automatic identification of spatially interacting motifs among distantly related proteins sharing similar folds and possessing common ancestral lineage. Spatial interactions between conserved stretches of a protein are evaluated by calculations of pseudo-potentials that describe the strength of interactions. Such an evaluation permits the automatic identification of highly interacting conserved regions of a protein. Interacting motifs have been shown to be useful in searching for distant homologues and establishing remote homologies among the largely unassigned sequences in genome databases. Information on such motifs should also be of value in protein folding, modelling and engineering experiments. The iMOT server can be accessed from http://www.ncbs.res.in/~faculty/mini/imot/IMOTserver.html. Supplementary Material can be accessed from: http://www.ncbs.res.in/~faculty/mini/imot/supplementary.html.

    Original languageEnglish (US)
    JournalNucleic acids research
    Volume32
    Issue numberWEB SERVER ISS.
    DOIs
    StatePublished - Jul 1 2004

    ASJC Scopus subject areas

    • Genetics

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