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This article is part of the supplement: The Second Automated Function Prediction Meeting

Open Access Proceedings

The AnnoLite and AnnoLyze programs for comparative annotation of protein structures

Marc A Marti-Renom1*, Andrea Rossi2, Fátima Al-Shahrour3, Fred P Davis2, Ursula Pieper2, Joaquín Dopazo3 and Andrej Sali2

Author Affiliations

1 Structural Genomics Unit, Bioinformatics Department, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain

2 Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry, and California Institute for Quantitative Biomedical Research, University of California at San Francisco, San Francisco, CA 94143, USA

3 Functional Genomics Unit, Bioinformatics Department, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain

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BMC Bioinformatics 2007, 8(Suppl 4):S4  doi:10.1186/1471-2105-8-S4-S4

Published: 22 May 2007

Abstract

Background

Advances in structural biology, including structural genomics, have resulted in a rapid increase in the number of experimentally determined protein structures. However, about half of the structures deposited by the structural genomics consortia have little or no information about their biological function. Therefore, there is a need for tools for automatically and comprehensively annotating the function of protein structures. We aim to provide such tools by applying comparative protein structure annotation that relies on detectable relationships between protein structures to transfer functional annotations. Here we introduce two programs, AnnoLite and AnnoLyze, which use the structural alignments deposited in the DBAli database.

Description

AnnoLite predicts the SCOP, CATH, EC, InterPro, PfamA, and GO terms with an average sensitivity of ~90% and average precision of ~80%. AnnoLyze predicts ligand binding site and domain interaction patches with an average sensitivity of ~70% and average precision of ~30%, correctly localizing binding sites for small molecules in ~95% of its predictions.

Conclusion

The AnnoLite and AnnoLyze programs for comparative annotation of protein structures can reliably and automatically annotate new protein structures. The programs are fully accessible via the Internet as part of the DBAli suite of tools at http://salilab.org/DBAli/ webcite.