ArticleBMC bioinformatics2013
Function prediction from networks of local evolutionary similarity in protein structure.
Article in BMC bioinformatics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed, 14 citations in OpenAlex.
- An Evolutionary Trace method defines functionally important bases and sites common to RNA families.PLoS computational biology · 2020Article
- A partially function-to-topic model for protein function prediction.BMC genomics · 2018Article
- Template-based prediction of protein function.Current opinion in structural biology · 2015Review
- Prediction of detailed enzyme functions and identification of specificity determining residues by random forests.PloS one · 2014Article
- Prediction and redesign of protein-protein interactions.Progress in biophysics and molecular biologyReview
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
Abstract
backgroundAnnotating protein function with both high accuracy and sensitivity remains a major challenge in structural genomics. One proven computational strategy has been to group a few key functional amino acids into templates and search for these templates in other protein structures, so as to transfer function when a match is found. To this end, we previously developed Evolutionary Trace Annotation (ETA) and showed that diffusing known annotations over a network of template matches on a structural genomic scale improved predictions of function. In order to further increase sensitivity, we now let each protein contribute multiple templates rather than just one, and also let the template size vary.
resultsRetrospective benchmarks in 605 Structural Genomics enzymes showed that multiple templates increased sensitivity by up to 14% when combined with single template predictions even as they maintained the accuracy over 91%. Diffusing function globally on networks of single and multiple template matches marginally increased the area under the ROC curve over 0.97, but in a subset of proteins that could not be annotated by ETA, the network approach recovered annotations for the most confident 20-23 of 91 cases with 100% accuracy.
conclusionsWe improve the accuracy and sensitivity of predictions by using multiple templates per protein structure when constructing networks of ETA matches and diffusing annotations.
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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.