title: ArchDB: automated protein loop classification as a tool for structural genomics.
abstract: The annotation of protein function has become a crucial problem with the advent of sequence and structural genomics initiatives. A large body of evidence suggests that protein structural information is frequently encoded in local sequences, and that folds are mainly made up of a number of simple local units of super-secondary structural motifs, consisting of a few secondary structures and their connecting loops. Moreover, protein loops play an important role in protein function. Here we present ArchDB, a classification database of structural motifs, consisting of one loop plus its bracing secondary structures. ArchDB currently contains 12,665 super-secondary elements classified into 1496 motif subclasses. The database provides an easy way to retrieve functional information from protein structures sharing a common motif, to search motifs found in a given SCOP family, superfamily or fold, or to search by keywords on proteins with classified loops. The ArchDB database of loops is located at http://sbi.imim.es/archdb.
authors.affiliation: Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.
authors.forename: Jordi
authors.initials: J
authors.lastname: Espadaler
authors.forename: Narcis
authors.initials: N
authors.lastname: Fernandez-Fuentes
authors.forename: Antonio
authors.initials: A
authors.lastname: Hermoso
authors.forename: Enrique
authors.initials: E
authors.lastname: Querol
authors.forename: Francesc X
authors.initials: FX
authors.lastname: Aviles
authors.forename: Michael J E
authors.initials: MJ
authors.lastname: Sternberg
authors.forename: Baldomero
authors.initials: B
authors.lastname: Oliva
mesh_terms: D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D000818:Animals; D001331:Automation; D019295:Computational Biology; D030562:Databases, Protein; D023281:Genomics; D006801:Humans; D020407:Internet; D008969:Molecular Sequence Data; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry* / Q000145:classification* / Q000378:metabolism
chemical_list: D011506:Proteins