ArticleJournal of molecular biology2010
Evolutionary trace annotation of protein function in the structural proteome.
Article in Journal of molecular biology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- Article
- Protein Structure Inspired Drug Discovery.bioRxiv : the preprint server for biology · 2024Article
- Recurrent high-impact mutations at cognate structural positions in class A G protein-coupled receptors expressed in tumors.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Article
- Evolutionary action and structural basis of the allosteric switch controlling βNature communications · 2017Article
- Objective assessment of the evolutionary action equation for the fitness effect of missense mutations across CAGI-blinded contests.Human mutation · 2017Review
- Proteins and Their Interacting Partners: An Introduction to Protein-Ligand Binding Site Prediction Methods.International journal of molecular sciences · 2015Review
- Evolutionary Action Score of TP53 Identifies High-Risk Mutations Associated with Decreased Survival and Increased Distant Metastases in Head and Neck Cancer.Cancer research · 2015Article
- A formal perturbation equation between genotype and phenotype determines the Evolutionary Action of protein-coding variations on fitness.Genome research · 2014Article
- Prediction and experimental validation of enzyme substrate specificity in protein structures.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Accounting for epistatic interactions improves the functional analysis of protein structures.Bioinformatics (Oxford, England) · 2013Article
- Are predicted protein structures of any value for binding site prediction and virtual ligand screening?Current opinion in structural biology · 2013Review
- Function prediction from networks of local evolutionary similarity in protein structure.BMC bioinformatics · 2013Article
- Statistical discovery of site inter-dependencies in sub-molecular hierarchical protein structuring.EURASIP journal on bioinformatics & systems biology · 2012Article
- The use of evolutionary patterns in protein annotation.Current opinion in structural biology · 2012Review
- Structure-based functional inference of hypothetical proteins from Mycoplasma hyopneumoniae.Journal of molecular modeling · 2012Article
- Exploring functionally related enzymes using radially distributed properties of active sites around the reacting points of bound ligands.BMC structural biology · 2012Article
- CLIPS-1D: analysis of multiple sequence alignments to deduce for residue-positions a role in catalysis, ligand-binding, or protein structure.BMC bioinformatics · 2012Article
- Evolutionary trace for prediction and redesign of protein functional sites.Methods in molecular biology (Clifton, N.J.) · 2012Article
- Protein function prediction: towards integration of similarity metrics.Current opinion in structural biology · 2011Review
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4 authors.
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Abstract
By design, structural genomics (SG) solves many structures that cannot be assigned function based on homology to known proteins. Alternative function annotation methods are therefore needed and this study focuses on function prediction with three-dimensional (3D) templates: small structural motifs built of just a few functionally critical residues. Although experimentally proven functional residues are scarce, we show here that Evolutionary Trace (ET) rankings of residue importance are sufficient to build 3D templates, match them, and then assign Gene Ontology (GO) functions in enzymes and non-enzymes alike. In a high-specificity mode, this Evolutionary Trace Annotation (ETA) method covered half (53%) of the 2384 annotated SG protein controls. Three-quarters (76%) of predictions were both correct and complete. The positive predictive value for all GO depths (all-depth PPV) was 84%, and it rose to 94% over GO depths 1-3 (depth 3 PPV). In a high-sensitivity mode, coverage rose significantly (84%), while accuracy fell moderately: 68% of predictions were both correct and complete, all-depth PPV was 75%, and depth 3 PPV was 86%. These data concur with prior mutational experiments showing that ET rank information identifies key functional determinants in proteins. In practice, ETA predicted functions in 42% of 3461 unannotated SG proteins. In 529 cases--including 280 non-enzymes and 21 for metal ion ligands--the expected accuracy is 84% at any GO depth and 94% down to GO depth 3, while for the remaining 931 the expected accuracies are 60% and 71%, respectively. Thus, local structural comparisons of evolutionarily important residues can help decipher protein functions to known reliability levels and without prior assumption on functional mechanisms. ETA is available at http://mammoth.bcm.tmc.edu/eta.
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