ArticleProtein science : a publication of the Protein Society2004
Automated selection of positions determining functional specificity of proteins by comparative analysis of orthologous groups in protein families.
Article in Protein science : a publication of the Protein Society, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 62 papers.
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62 citing papers in PubMed, 115 citations in OpenAlex.
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- Paracellular and Transcellular Leukocytes Diapedesis Are Divergent but Interconnected Evolutionary Events.Genes · 2021Article
- Bioinformatic analysis of subfamily-specific regions in 3D-structures of homologs to study functional diversity and conformational plasticity in protein superfamilies.Computational and structural biotechnology journal · 2021Article
- Identification and Analysis of Unstructured, Linear B-Cell Epitopes in SARS-CoV-2 Virion Proteins for Vaccine Development.Vaccines · 2020Article
- DIP/Dpr interactions and the evolutionary design of specificity in protein families.Nature communications · 2020Article
- Deep Analysis of Residue Constraints (DARC): identifying determinants of protein functional specificity.Scientific reports · 2020Article
- Recognition of sites of functional specialisation in all known eukaryotic protein kinase families.PLoS computational biology · 2018Article
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- Inference of Functionally-Relevant N-acetyltransferase Residues Based on Statistical Correlations.PLoS computational biology · 2016Article
- Structure-guided selection of specificity determining positions in the human Kinome.BMC genomics · 2016Article
- Genomic Analysis of the Human Gut Microbiome Suggests Novel Enzymes Involved in Quinone Biosynthesis.Frontiers in microbiology · 2016Article
- pocketZebra: a web-server for automated selection and classification of subfamily-specific binding sites by bioinformatic analysis of diverse protein families.Nucleic acids research · 2014Article
- Systematic genomic analysis reveals the complementary aerobic and anaerobic respiration capacities of the human gut microbiota.Frontiers in microbiology · 2014Article
- Comparative genomics and evolution of regulons of the LacI-family transcription factors.Frontiers in microbiology · 2014Article
- Functional diversification of ROK-family transcriptional regulators of sugar catabolism in the Thermotogae phylum.Nucleic acids research · 2013Article
- Multiple co-evolutionary networks are supported by the common tertiary scaffold of the LacI/GalR proteins.PloS one · 2013Article
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2 more citing papers are in PubMed but not listed here.
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4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The increasing volume of genomic data opens new possibilities for analysis of protein function. We introduce a method for automated selection of residues that determine the functional specificity of proteins with a common general function (the specificity-determining positions [SDP] prediction method). Such residues are assumed to be conserved within groups of orthologs (that may be assumed to have the same specificity) and to vary between paralogs. Thus, considering a multiple sequence alignment of a protein family divided into orthologous groups, one can select positions where the distribution of amino acids correlates with this division. Unlike previously published techniques, the introduced method directly takes into account nonuniformity of amino acid substitution frequencies. In addition, it does not require setting arbitrary thresholds. Instead, a formal procedure for threshold selection using the Bernoulli estimator is implemented. We tested the SDP prediction method on the LacI family of bacterial transcription factors and a sample of bacterial water and glycerol transporters belonging to the major intrinsic protein (MIP) family. In both cases, the comparison with available experimental and structural data strongly supported our predictions.
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