The FSSP database: fold classification based on structure-structure alignment of proteins.
The FSSP database presents a continuously updated classification of 3-D protein folds based on an all-against-all comparison of structures currently in the Protein Data Bank (PDB) [Bernstein et al. (1977) J. Mol. Biol., 112, 535- 542]. The database currently contains an extended structural family for each of 600 representative protein chains which have <25% mutual sequence identity. The results of the exhaustive pairwise structure comparisons are reported in the form of a fold tree generated by hierarchical clustering and as a series of structurally representative sets of folds at varying levels of uniqueness. For each query structure from the representative set, there is a database entry containing structure-structure alignments with its structural neighbours in the representative set and its sequence homologs in the PDB. All alignments are based purely on the 3-D co-ordinates of the proteins and are derived by an automatic structure comparison program (Dali). The FSSP database is accessible electronically on the World Wide Web and by anonymous ftp.
Holm
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European Molecular Biology Laboratory, Heidelberg, Germany.
Sander
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C
D000595:Amino Acid Sequence; D000818:Animals; D003195:Computer Communication Networks; D016208:Databases, Factual; D006801:Humans; D008969:Molecular Sequence Data; D017510:Protein Folding; D016415:Sequence Alignment