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  1. PASS2
    Resource Category : Databases -> Structure Databases -> Protein structure

    Brief Description : The Protein Alignments organised as Structural Superfamily (PASS2) database represent continuously updated, structure-based alignments for evolutionary related, sequentially distant proteins. The automated and updated version of PASS2, is in direct correspondence with SCOP 1.63, consisting of sequences having identity below 40% among themselves. Protein domains are grouped in 628 multi-member superfamilies and 566 single member superfamiles. Structure based sequence alignments for the superfamilies have been obtained using COMPARER, where initial equivalences have been derived from a preliminary superposition using LSQMAN or STAMP 4.0. The final sequence alignments have been annotated for structural features using JOY 4.0. The database is supplemented with sequence relatives belonging to different genomes, conserved spatially interacting and structural motifs, probabilistic hidden markov models of superfamilies based on the alignments and useful links to other databases. The database resolves alignments among the structural domains consisting of evolutionarily diverged set of sequences. PASS2 organisation of protein superfamilies provides a map of known regions of the protein universe, useful for the analysis of protein folds, for evolutionary unification of protein families and maximizing the information return from experimental structure determination. Probabilistic models and sensitive position specific profiles obtained from reliable superfamily alignments aids annotation of remote homologues and are useful tools in structural and functional genomics. PASS2 is accessible at http://www.ncbs.res.in/~faculty/mini/campass/pass2.html.

    Institute/s :
    National centre for Biological Sciences (TIFR), GKVK campus, Bangalore 560 065, Karnataka, India
    Address of Institute/s :
    National centre for Biological Sciences (TIFR), GKVK campus, Bangalore 560 065, Karnataka, India
    State : Karnataka
    Country : India

    Associated Institutes :

    • National centre for Biological Sciences (TIFR), GKVK campus, Bangalore 560 065, Karnataka, India

    Associated Country : India


    Authors/Contributors : A. Gandhimathi; Anu G. Nair; R. Sowdhamini
    Contact Email : mini@ncbs.res.in
    Year : 2011
    Language : English