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NAR Molecular Biology Database Collection entry number 275
Sowdhamini, Ramanathan; Gandhimathi, Arumugam; Nair, Anu
National Centre for Biological Sciences, Tata Institute for Fundamental Research, UAS-GKVK campus, Bangalore 560 065, India

Database 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

Recent Developments

Structural motifs, which are conserved amino acid residues probably important for the fold integrity, have been identified and annotated for all multi-member superfamilies in PASS2. Graphical interface for the inspection of motifs and the preservation of structural features of the motifs are provided. Structural motifs can be of value in protein fold recognition and in comparative modelling.


This work is supported by the International Senior Fellowship to RS from the Wellcome Trust, London.


1. Sowdhamini, R., Burke, D.F., Huang, J., Mizuguchi, K., Nagarajaram, H.A., Steward, R.E. & Blundell, T.L. (1998). CAMPASS: A database of structurally aligned protein superzamilies. Structure, 6, 1087-1094.
2. Murzin, A.G., Brenner, S.E., Hubbard, T. & Chothia, C. (1995). SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol., 247, 536-540.
3. Mallika, V., Bhaduri, A. and Sowdhamini, R.(2002) PASS2: a semi-automated database of Protein Alignments organised as Structural Superfamilies. Nucleic Acids Res., 30, 284-288.

Subcategory: Protein structure

Go to the abstract in the NAR 2012 Database Issue.
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