Latest version in correspondence with SCOP 1.73 release

Last modified :1st Oct 2008

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About the database

PASS2 is an automatic version of the original superfamily alignment database, CAMPASS (CAMbridge database of Protein Alignments organised as Structural Superfamilies, Sowdhamini et al., 1998). PASS2 contains alignments of protein structures at the superfamily level and is in direct correspondence with SCOP 1.73 release (Structural Classification Of Proteins, Murzin et al.,1995).

Protein (Domain)s in the database

SCOP superfamilies have been considered for the curation of the database. Members of the database share no more than 40% sequence identity among themselves. Alignments for the multi-member superfamilies are based on conservation of structural features like solvent accessibility, hydrogen bonding and the presence of secondary structures. A preliminary superposition has been done using MINRMS (Jewett et al., 2003) and STAMP (Russell et al., 1992) for two member and multi member superfamilies respectively. Deriving initial equivalences from the alignment, a refined structural alignment is done using COMPARER (Sali et al., 1990; Sali et al.,1992). The final alignment is presented in JOY format (Mizuguchi et al., 1998) to display three-dimensional (3D) structural features.

We have classified our superfamilies into single member, two member and multi member superfamilies. The current version contains 676 multi member superfamilies, 327 two member superfamilies and 773 structure based sequence annotated single member superfamilies. Sequence members for the superfamilies in different genomes have been listed and aligned. Links have been provided to the conserved interacting motifs and the hidden markov models for the different superfamilies present in PASS2. Sequence alignment with PASS2 members are possible using MALIGN. Sequence searches against the PASS2 database using PSI-BLAST and PHI-BLAST can also be pursued. Prediction of a superfamily based on structural compatibility can also be performed. Each entry of PASS2 has been linked to other databases and tools for easy access of information.

New features:

    CUSP:  An algorithm to distinguish structurally conserved and unconserved regions in protein domain alignments and its application in the study of large length variations     Reference

    SMotif:  Structural segments or motifs for a given protein structure(s) based on conservation of both sequential as well as important structural features such as solvent inaccessibility, secondary structural content, hydrogen bonding pattern and residue packing    Reference

    PCA: The principal component analysis, a vector space transform often used to reduce multidimensionality of datasets.  

    Alistat: A statistical calculation for the alignment of core structural members  

    README: The README file in each superfamily will briefly describes about the total number of members, the number of members in the core alignment, the method of creation of core alignment for that particular superfamily and the available downloads for each superfamily  

Number of Single Member, Two member and Multi Member Superfamilies

S. No Class Number of
Number of
Number of
1 All Alpha Proteins(all a) 241 82 136 459
2 All Beta Proteins(all b) 140 54 137 331
3 Alpha and Beta Proteins(a/b) 56 40 136 232
4 Alpha and Beta Proteins(a+b) 198 97 192 487
5 Multi-Domain Proteins(a&b) 25 13 15 53
6 Membrane and cell surface proteins and peptides 57 19 16 92
7 Small Proteins 56 22 44 122
Total 773 327 676 1776

How to cite previous PASS2 databases

Bhaduri A, Pugalenthi G, Sowdhamini R. PASS2: an automated database of protein alignments organised as structural superfamilies. BMC Bioinformatics. 2004, 5:35

V. Mallika, Anirban Bhaduri and R. Sowdhamini. PASS2: a semi-automated database of Protein Alignments Organised as Structural Superfamilies. Nucleic Acids Research, 2002, 30(1): 284-288

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Your suggestions and further clarifications are most welcome.
Please send a mail to
PASS2 group:
Prof. R. Sowdhamini K. Kanagarajadurai P. Nagarajan S. Kalaimathy