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Nucleic Acids Research, 2004, Vol. 32, Database issue D185-D188
© 2004 Oxford University Press

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

Jordi Espadaler1,2, Narcis Fernandez-Fuentes1,3, Antonio Hermoso1, Enrique Querol1, Francesc X. Aviles1, Michael J. E. Sternberg3 and Baldomero Oliva*,2

1 Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica, Universitat Autònoma de Barcelona, 08193 Bellaterra (Barcelona), Spain, 2 Laboratori de Bioinformàtica Estructural, Grup de Recerca d’Informàtica Biomédica—IMIM, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, C/Doctor Aiguader 80, Barcelona 08003, Catalonia, Spain and 3 Structural Bioinformatics Group, Biochemistry Building, Department of Biological Sciences, Imperial College, London SW7 2AZ, UK

*To whom correspondence should be addressed. Tel: +34 93 2240880; Fax: +34 93 2240875; Email: boliva{at}imim.es

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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