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.
|Journal||Nucleic Acids Research|
|Issue number||DATABASE ISS.|
|Publication status||Published - 1 Jan 2004|
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.).