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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59 Citations (Scopus)

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.
Original languageEnglish
JournalNucleic Acids Research
Volume32
Issue numberDATABASE ISS.
Publication statusPublished - 1 Jan 2004

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    Espadaler, J., Fernandez-Fuentes, N., Hermoso, A., Querol, E., Aviles, F. X., Sternberg, M. J. E., & Oliva, B. (2004). ArchDB: Automated protein loop classification as a tool for structural genomics. Nucleic Acids Research, 32(DATABASE ISS.).