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Bioinformatics Advance Access originally published online on July 26, 2006
Bioinformatics 2006 22(18):2237-2243; doi:10.1093/bioinformatics/btl382
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© The Author 2006. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Identification of function-associated loop motifs and application to protein function prediction

Jordi Espadaler 1,2, Enrique Querol 2, Francesc X. Aviles 2 and Baldo Oliva 1,*

1 Grup de Bioinformàtica Estructural (GRIB-IMIM), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra 08003 Barcelona, Catalonia, Spain
2 Institut de Biotecnologia i Biomedicina and Departament de Bioquímica, Universitat Autònoma de Barcelona, 08193 Bellaterra (Barcelona) Catalonia, Spain

*To whom correspondence should be addressed.

Motivation: The detection of function-related local 3D-motifs in protein structures can provide insights towards protein function in absence of sequence or fold similarity. Protein loops are known to play important roles in protein function and several loop classifications have been described, but the automated identification of putative functional 3D-motifs in such classifications has not yet been addressed. This identification can be used on sequence annotations.

Results: We evaluated three different scoring methods for their ability to identify known motifs from the PROSITE database in ArchDB. More than 500 new putative function-related motifs not reported in PROSITE were identified. Sequence patterns derived from these motifs were especially useful at predicting precise annotations. The number of reliable sequence annotations could be increased up to 100% with respect to standard BLAST.

Contact: boliva{at}imim.es

Supplementary information: Supplementary Data are available at Bioinformatics online.

Received on March 30, 2006; revised on July 4, 2006; accepted on July 6, 2006

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