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

Research output: Contribution to journalArticleResearchpeer-review

61 Citations (Scopus)


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


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