ArticleBioinformatics (Oxford, England)2009
Evolutionary Trace Annotation Server: automated enzyme function prediction in protein structures using 3D templates.
Article in Bioinformatics (Oxford, England), 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- EnzymeHunter: Achieving fine-grained enzyme function prediction with a hierarchically aware contrastive learning framework.Patterns (New York, N.Y.) · 2026Article
- Rheostats, toggles, and neutrals, Oh my! A new framework for understanding how amino acid changes modulate protein function.The Journal of biological chemistry · 2024Review
- Capturing the geometry, function, and evolution of enzymes with 3D templates.Protein science : a publication of the Protein Society · 2022Review
- PANNZER-A practical tool for protein function prediction.Protein science : a publication of the Protein Society · 2022Article
- Objective assessment of the evolutionary action equation for the fitness effect of missense mutations across CAGI-blinded contests.Human mutation · 2017Review
- A formal perturbation equation between genotype and phenotype determines the Evolutionary Action of protein-coding variations on fitness.Genome research · 2014Article
- Structure prediction of partial-length protein sequences.International journal of molecular sciences · 2013Article
- Function prediction from networks of local evolutionary similarity in protein structure.BMC bioinformatics · 2013Article
- ETAscape: analyzing protein networks to predict enzymatic function and substrates in Cytoscape.Bioinformatics (Oxford, England) · 2012Article
- SPEER-SERVER: a web server for prediction of protein specificity determining sites.Nucleic acids research · 2012Article
- Exploring functionally related enzymes using radially distributed properties of active sites around the reacting points of bound ligands.BMC structural biology · 2012Article
- Getting personalized cancer genome analysis into the clinic: the challenges in bioinformatics.Genome medicine · 2012Review
- Virtual interactomics of proteins from biochemical standpoint.Molecular biology international · 2012Article
- Protein function prediction: towards integration of similarity metrics.Current opinion in structural biology · 2011Review
- A new approach to assess and predict the functional roles of proteins across all known structures.Journal of structural and functional genomics · 2011Article
- Networks of high mutual information define the structural proximity of catalytic sites: implications for catalytic residue identification.PLoS computational biology · 2010Article
- Sequence and structure continuity of evolutionary importance improves protein functional site discovery and annotation.Protein science : a publication of the Protein Society · 2010Article
- Evolution: a guide to perturb protein function and networks.Current opinion in structural biology · 2010Review
- Evolution-guided discovery and recoding of allosteric pathway specificity determinants in psychoactive bioamine receptors.Proceedings of the National Academy of Sciences of the United States of America · 2010Article
- Ensemble approach to predict specificity determinants: benchmarking and validation.BMC bioinformatics · 2009Article
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
summaryThe 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/).
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.