Evolutionary Trace Annotation Server: automated enzyme function prediction in protein structures using 3D templates
| Autor: | R. Matthew Ward, David M. Kristensen, Stephen C. Murray, Eric Venner, Serkan Erdin, Olivier Lichtarge, Bryce Daines |
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| Rok vydání: | 2009 |
| Předmět: |
Statistics and Probability
Protein Conformation Computational biology Biology Biochemistry Structural genomics Evolution Molecular 03 medical and health sciences Annotation Molecular evolution Phylogenetics Web application Databases Protein Molecular Biology Phylogeny 030304 developmental biology Internet 0303 health sciences Phylogenetic tree business.industry 030302 biochemistry & molecular biology Structure function Computational Biology Proteins Structural Bioinformatics Predictive value Enzymes Computer Science Applications Applications Note Computational Mathematics Computational Theory and Mathematics business Algorithm Software |
| Zdroj: | Bioinformatics |
| ISSN: | 1367-4811 1367-4803 |
| Popis: | 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 (ET) method to extract key functional residues and propose a function-associated 3D 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 next 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. Users may modify any search parameter, including the template. ETA thus expands the ET suite for protein structure annotation, 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/. Contact: lichtarge@bcm.edu |
| Databáze: | OpenAIRE |
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