This database consists of clusters of potentially related homologous protein domain families, with and without three-dimensional structural information, forming superfamilies. The present release (Release 6.0) of SUPFAM uses homologous families in Pfam (Version 27.0) and SCOP (version 1.75) which are examples of sequence -alignment and structure classification databases respectively.
The two steps involved in setting up of SUPFAM database are
- Relating Pfam and SCOP families using a new profile-profile alignment algorithm AlignHUSH. This results in identifying many Pfam families which could be related to a family or superfamily of known structural information.
- An all-against-all match among Pfam families with yet unknown structure resulting in identification of related Pfam families forming new potential superfamilies.
The statistics link gives the details of the success of the SUPFAM approach.
The SUPFAM database can be used in either the Browse mode or Search mode (see menu on left).
In Browse mode you can browse through the Superfamilies, Pfam families or SCOP families. In each of these modes you will be presented with a full list which can be easily browsed.
In Search mode, you can search for Pfam families, SCOP families or Superfamilies based on keywords or SCOP/Pfam identifiers of families and superfamilies.
New Features of SUPFAM web-site
- Updated databases - Pfam database (version 27.0) and SCOP database (version 1.75)
- Use of ALignHUSH profile-profile alignment program to relate families and a more rigrous decision tree
- Graphical representation of superfamilies has been added.
- Indirect mappings of Pfam families to SCOP superfamily are also displayed.
- Graphical interface (Jmol applet) for representative structures of SCOP families has been added.
- SUPFAM - Database of potential protein superfamily relationships derived by comparing sequence-based and structure-based families: Implications for structural genomics and function annotation in genomes. Shashi B. Pandit, Dilip Gosar, S. Abhiman, S. Sujatha, Sayali S. Dixit, Natasha S. Mhatre, R. Sowdhamini and N. Srinivasan. Nucleic Acids Research. 2002, 30: 289-293.
- SUPFAM: a database of sequence superfamilies of protein domains. Pandit SB, Bhadra R, Gowri VS, Balaji S, Anand B, Srinivasan N. BMC Bioinformatics. 2004 Mar 15, 5-28.
- Recognition of remotely related structural homologues using sequence profiles of aligned homologous protein structures. Namboori S, Srinivasan N, Pandit SB. In Silico Biol. 2004 4(4): 445-60.
- AlignHUSH: Alignment of HMMs using structure and hydrophobicity information. Krishnadev o., and Srinivasan N. BMC Bioinformatics. 2011, 12, 275