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The AnnoLite and AnnoLyze programs for comparative annotation of protein structures

, 1 , 2 , 3 , 2 , 2 , 3 , 2

BMC Bioinformatics

BioMed Central

The Second Automated Function Prediction Meeting

30 August – 1 September 2006

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      Abstract

      BackgroundAdvances 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.DescriptionAnnoLite 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.ConclusionThe 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 .

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            Author and article information

            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
            Contributors
            Conference
            BMC Bioinformatics
            BMC Bioinformatics
            BioMed Central (London )
            1471-2105
            2007
            22 May 2007
            : 8
            : Suppl 4
            : S4
            1892083
            17570147
            1471-2105-8-S4-S4
            10.1186/1471-2105-8-S4-S4
            Copyright © 2007 Marti-Renom et al; licensee BioMed Central Ltd.

            This is an open access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

            The Second Automated Function Prediction Meeting
            La Jolla, CA, USA
            30 August – 1 September 2006
            Categories
            Proceedings

            Bioinformatics & Computational biology

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