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 1.63 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 LSQMAN (Kleywegt et al.,1994) or STAMP (Russell et al., 1992). Deriving initial equivalences from the alignment, a refined structural alignment is done using COMPARER (Sali etal., 1990; Sali et al.,1992). The final alignment are presented in JOY format (Mizuguchi et al., 1998) to display three-dimensional (3D).


The current version contains 628 multi member superfamilies and 566 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 and JOY. Sequence searches against the PASS2 database using PSI-BLAST and PHI-BLAST can also be persued. 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.

• Information about PASS2
  
  
• Superfamily list :
  
     * single member superfamilies     * multi member superfamilies
  
  
• Search PASS2.
  
  
• Align Your Sequence with PASS2 Members.
  
  
• Useful Tools
  
  
• Help file
  
  
• CAMPASS (old version 1998) and PASS2(previous version 2002)
  
  

*New features:

• Predict superfamily of query  
  
  
• Align Sturcture to a given Superfamily  
  
  
• Sequence and Structural phylogeny of the PASS2 Members  
  
  
• Hidden Markov Models based on the structural Alignment  
  
  
• Interacting Motifs of the PASS2 members  
  
  
• Improved Search facility  
  
  
• Genomic Search based on PSI-BLAST and Hmmsearch  
  
  

Number of Single Member and Multi Member Superfamilies

S.No	Class	Number Of SMS	Number of MMS
1	All Alpha Proteins(all a)	161	129
2	All Beta Proteins(all b)	105	131
3	Alpha and Beta Proteins(a/b)	158	176
4	Alpha and Beta Proteins(a+b)	73	120
5	Multi-Domain Proteins(a&b)	22	14
6	Membrane Proteins	10	7
7	Small Proteins	37	51

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Your suggestions and further clarifications are most welcome.

-please send a mail to mini@ncbs.res.in

PASS2 group: 

     Dr.R.Sowdhamini
     Anirban Bhaduri
     G.Pugalenthi