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


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.

SUBMITTER: Espadaler J 

PROVIDER: S-EPMC308737 | biostudies-literature | 2004 Jan

REPOSITORIES: biostudies-literature

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

Espadaler Jordi J   Fernandez-Fuentes Narcis N   Hermoso Antonio A   Querol Enrique E   Aviles Francesc X FX   Sternberg Michael J E MJ   Oliva Baldomero B  

Nucleic acids research 20040101 Database issue


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  ...[more]

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