ArticlePLoS computational biology2009
FLORA: a novel method to predict protein function from structure in diverse superfamilies.
Article in PLoS computational biology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed.
- Integrating evidence from protein domains to identify cancer driver mutations.Protein science : a publication of the Protein Society · 2026Article
- Structure and Expression Analysis ofInternational journal of molecular sciences · 2023Article
- Engagement of intrinsic disordered proteins in protein-protein interaction.Frontiers in molecular biosciences · 2023Article
- Bioinformatics analysis of3 Biotech · 2021Article
- Identification and Characterization of theGenes · 2021Article
- Multi-criteria protein structure comparison and structural similarities analysis using pyMCPSC.PloS one · 2018Article
- Structure-guided selection of specificity determining positions in the human Kinome.BMC genomics · 2016Article
- Molecular annotation of ketol-acid reductoisomerases from Streptomyces reveals a novel amino acid biosynthesis interlock mediated by enzyme promiscuity.Microbial biotechnology · 2015Article
- Estimation of protein function using template-based alignment of enzyme active sites.BMC bioinformatics · 2014Article
- Prediction of detailed enzyme functions and identification of specificity determining residues by random forests.PloS one · 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
- Functional site plasticity in domain superfamilies.Biochimica et biophysica acta · 2013Article
- Recent advances in functional region prediction by using structural and evolutionary information - Remaining problems and future extensions.Computational and structural biotechnology journal · 2013Review
- ETAscape: analyzing protein networks to predict enzymatic function and substrates in Cytoscape.Bioinformatics (Oxford, England) · 2012Article
- Structure- and sequence-based function prediction for non-homologous proteins.Journal of structural and functional genomics · 2012Article
- The use of evolutionary patterns in protein annotation.Current opinion in structural biology · 2012Review
- Exploring functionally related enzymes using radially distributed properties of active sites around the reacting points of bound ligands.BMC structural biology · 2012Article
- Evolutionary trace for prediction and redesign of protein functional sites.Methods in molecular biology (Clifton, N.J.) · 2012Article
- Article
- Gene3D: a domain-based resource for comparative genomics, functional annotation and protein network analysis.Nucleic acids research · 2012Article
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5 authors.
Funding
Abstract
Predicting protein function from structure remains an active area of interest, particularly for the structural genomics initiatives where a substantial number of structures are initially solved with little or no functional characterisation. Although global structure comparison methods can be used to transfer functional annotations, the relationship between fold and function is complex, particularly in functionally diverse superfamilies that have evolved through different secondary structure embellishments to a common structural core. The majority of prediction algorithms employ local templates built on known or predicted functional residues. Here, we present a novel method (FLORA) that automatically generates structural motifs associated with different functional sub-families (FSGs) within functionally diverse domain superfamilies. Templates are created purely on the basis of their specificity for a given FSG, and the method makes no prior prediction of functional sites, nor assumes specific physico-chemical properties of residues. FLORA is able to accurately discriminate between homologous domains with different functions and substantially outperforms (a 2-3 fold increase in coverage at low error rates) popular structure comparison methods and a leading function prediction method. We benchmark FLORA on a large data set of enzyme superfamilies from all three major protein classes (alpha, beta, alphabeta) and demonstrate the functional relevance of the motifs it identifies. We also provide novel predictions of enzymatic activity for a large number of structures solved by the Protein Structure Initiative. Overall, we show that FLORA is able to effectively detect functionally similar protein domain structures by purely using patterns of structural conservation of all residues.
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