ArchDB: automated protein loop classification as a tool for structural genomics.

Jordi Espadaler; Narcis Fernandez-Fuentes; Antonio Hermoso; Enrique Querol; Francesc X Aviles; Michael J E Sternberg; Baldomero Oliva

doi:10.1093/nar/gkh002

PubMed · 14681390

ArchDB: automated protein loop classification as a tool for structural genomics.

Jordi Espadaler·Narcis Fernandez-Fuentes·Antonio Hermoso·Enrique Querol·Francesc X Aviles·Michael J E Sternberg·Baldomero Oliva

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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.

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Amino Acid Motifs Amino Acid Sequence Animals Automation Computational Biology Databases, Protein Genomics Humans Internet Molecular Sequence Data Protein Structure, Secondary Proteins Journal Article Research Support, Non-U.S. Gov't

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Jordi Espadaler, Narcis Fernandez-Fuentes, Antonio Hermoso, Enrique Querol, Francesc X Aviles, Michael J E Sternberg, Baldomero Oliva. 2004-01-01. ArchDB: automated protein loop classification as a tool for structural genomics.. https://doi.org/10.1093/nar%2Fgkh002

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