ArticleJournal of molecular biology2007
Functional specificity lies within the properties and evolutionary changes of amino acids.
Article in Journal of molecular biology, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed.
- MHC-II alleles shape the CDR3 repertoires of conventional and regulatory naïve CD4Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- DIP/Dpr interactions and the evolutionary design of specificity in protein families.Nature communications · 2020Article
- Recognition of sites of functional specialisation in all known eukaryotic protein kinase families.PLoS computational biology · 2018Article
- Molecular Evolution and Functional Divergence of the IgLON Family.Evolutionary bioinformatics online · 2018Article
- Massive expansion and differential evolution of small heat shock proteins with wheat (Triticum aestivum L.) polyploidization.Scientific reports · 2017Article
- Cyclic di-GMP mediates a histidine kinase/phosphatase switch by noncovalent domain cross-linking.Science advances · 2016Article
- Phylogenetic-Derived Insights into the Evolution of Sialylation in Eukaryotes: Comprehensive Analysis of Vertebrate β-Galactoside α2,3/6-Sialyltransferases (ST3Gal and ST6Gal).International journal of molecular sciences · 2016Review
- Correlated rigid modes in protein families.Physical biology · 2016Article
- Article
- SigniSite: Identification of residue-level genotype-phenotype correlations in protein multiple sequence alignments.Nucleic acids research · 2013Article
- Diversity of benzylsuccinate synthase-like (bssA) genes in hydrocarbon-polluted marine sediments suggests substrate-dependent clustering.Applied and environmental microbiology · 2013Article
- Article
- SPEER-SERVER: a web server for prediction of protein specificity determining sites.Nucleic acids research · 2012Article
- Automated hierarchical classification of protein domain subfamilies based on functionally-divergent residue signatures.BMC bioinformatics · 2012Article
- Cube-DB: detection of functional divergence in human protein families.Nucleic acids research · 2012Article
- New methods to measure residues coevolution in proteins.BMC bioinformatics · 2011Article
- Identification of family-determining residues in PHD fingers.Nucleic acids research · 2011Article
- Surveying the manifold divergence of an entire protein class for statistical clues to underlying biochemical mechanisms.Statistical applications in genetics and molecular biology · 2011Article
- An automated stochastic approach to the identification of the protein specificity determinants and functional subfamilies.Algorithms for molecular biology : AMB · 2010Article
- Article
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Authors and funding
3 authors.
Funding
Abstract
The rapid increase in the amount of protein sequence data has created a need for automated identification of sites that determine functional specificity among related subfamilies of proteins. A significant fraction of subfamily specific sites are only marginally conserved, which makes it extremely challenging to detect those amino acid changes that lead to functional diversification. To address this critical problem we developed a method named SPEER (specificity prediction using amino acids' properties, entropy and evolution rate) to distinguish specificity determining sites from others. SPEER encodes the conservation patterns of amino acid types using their physico-chemical properties and the heterogeneity of evolutionary changes between and within the subfamilies. To test the method, we compiled a test set containing 13 protein families with known specificity determining sites. Extensive benchmarking by comparing the performance of SPEER with other specificity site prediction algorithms has shown that it performs better in predicting several categories of subfamily specific sites.
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