SUPERFAMILY:HMMs representing all proteins of known structure

J. Gough, C. Chothia

Research output: Contribution to journalArticle (Academic Journal)peer-review


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 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.
Translated title of the contributionSUPERFAMILY:HMMs representing all proteins of known structure
Original languageEnglish
Article number268-272
JournalNucleic Acids Research
Volume30 (1)
Publication statusPublished - 2002

Bibliographical note

Other identifier: 1040021


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