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. 2004 Jan 1;32(Database issue):D185-8.
doi: 10.1093/nar/gkh002.

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

Jordi Espadaler  1 , Narcis Fernandez-Fuentes, Antonio Hermoso, Enrique Querol, Francesc X Aviles, Michael J E Sternberg, Baldomero Oliva
Affiliations

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

Jordi Espadaler et al. Nucleic Acids Res. .

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.

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Figures

Figure 1
Figure 1
Averaged RMSD between loops in subclasses. The averaged RMSD of the sets of loop structures on each subclass was calculated with the main-chain atoms of the residues in the loop plus two bracing residues at each side. Additional extensions of the bars show the standard deviations of the averages with the total loops involved in the RMSD calculation shown at the top. Due to the dramatic decrease in loops with length larger than 11 residues, the significance of the average RMSD is also waning.
Figure 2
Figure 2
Screenshot of ArchDB information HTML pages. Classification browser with subclass information, multiple alignments of sequence and conformation, the profile pattern and the image of no more than four structurally superimposed motifs as viewed with Rasmol (27).
See this image and copyright information in PMC

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