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Bioinformatics Advance Access published online on March 23, 2009
Bioinformatics, doi:10.1093/bioinformatics/btp160
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© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Evolutionary Trace Annotation (ETA) Server: Automated Enzyme Function Prediction in Protein Structures Using 3D Templates

R. Matthew Ward 1,2,5, Eric Venner 1,2, Bryce Daines 1, Stephen Murray 1, Serkan Erdin 1,5, David M. Kristensen 1,2,5 and Olivier Lichtarge 1,2,3,4,5,*

1Departments of Molecular and Human Genetics, 2Program in Structural and Computational Biology and Molecular Biophysics, 3Department of Biochemistry and Molecular Biology, 4Department of Pharmacology, One Baylor Plaza, Houston, TX 77030, 5W. M. Keck Center for Interdisciplinary Bioscience Training, Houston, TX 77005

*To whom correspondence should be addressed. Mr. R. Matthew Ward, E-mail: robert.ward{at}bcm.tmc.edu


  Abstract

Summary: The Evolutionary Trace Annotation (ETA) Server predicts enzymatic activity. ETA starts with a structure of unknown function, such as those from structural genomics, and with no prior knowledge of its mechanism uses the phylogenetic Evolutionary Trace method (ET) to extract key functional residues and propose a function-associated three-dimensional motif, called a 3D template. ETA then searches previously annotated structures for geometric template matches that suggest molecular and thus functional mimicry. In order to maximize the predictive value of these matches, ETA then applies distinctive specificity filters—evolutionary similarity, function plurality and match reciprocity. In large scale controls on enzymes, prediction coverage is 43% but the positive predictive value rises to 92%, thus minimizing false annotations (Ward, et al., 2008). Users may modify any search parameter including the template. ETA thus expands the ET suite for protein structure annotation (Mihalek, et al., 2006; Morgan, et al., 2006), and can contribute to the annotation efforts of metaservers.

Availability: The ETA Server is a web application available at http://mammoth.bcm.tmc.edu/eta/.

Associate Editor: Prof. Thomas Lengauer

Received on October 16, 2008; revised on February 6, 2009; accepted on March 16, 2009

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