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SUPERFAMILY


NAR Molecular Biology Database Collection entry number 285
Gough, J., Chothia, C.
MRC Laboratory of Molecular Biology Hills rd, Cambridge CB22QH, UK.

Database Description

The SUPERFAMILY database contains a library of hidden Markov models representing all proteins of known structure. The database is based on the SCOP 'superfamily' level of protein domain classification which groups together the most distantly related proteins which have a common evolutionary ancestor. There is a public server at http://supfam.org which provides three services: sequence searching, multiple alignments to sequences of known structure, and structural assignments to all complete genomes. Given an amino acid or nucleotide query sequence the server will return the domain architecture and SCOP classification. The server produces alignments of the query sequences with sequences of known structure, and includes multiple alignments of genome and PDB sequences. The structural assignments are carried out on all complete genomes (currently 59) covering approximately half of the soluble protein domains. The assignments, superfamily breakdown, and statistics on them are available from the server. The database is currently used by this group and others for genome annotation, structural genomics, gene prediction, and domain-based genomic studies.

Acknowledgements

Thanks to Thomas Down for help setting up the DAS server, and Matthew Bashton for contribution to web design.

References

Gough, J., Karplus, K., Hughey, R.,and Chothia, C. (2001). Assignment of Homology to Genome Sequences using a Library of Hidden Markov Models that Represent all Proteins of Known Structure. in press J. Mol. Biol. 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.

Subcategory: Protein structure

Go to the abstract in the NAR 2009 Database Issue.
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