ArticleMolecular biology and evolution2013
Integrating sequence variation and protein structure to identify sites under selection.
Article in Molecular biology and evolution, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed.
- High resolution immunoinformatic profiling of Zonula occludens toxin reveals a conserved multiepitope vaccine candidate inFrontiers in immunology · 2026Article
- Transcription factor binding sites are frequently under accelerated evolution in primates.Nature communications · 2023Article
- Site-Specific Amino Acid Distributions Follow a Universal Shape.Journal of molecular evolution · 2020Article
- Phylogenetic Modeling of Regulatory Element Turnover Based on Epigenomic Data.Molecular biology and evolution · 2020Article
- Structures and functions linked to genome-wide adaptation of human influenza A viruses.Scientific reports · 2019Article
- mtProtEvol: the resource presenting molecular evolution analysis of proteins involved in the function of Vertebrate mitochondria.BMC evolutionary biology · 2019Article
- A new parameter-rich structure-aware mechanistic model for amino acid substitution during evolution.Proteins · 2018Article
- Biophysical Models of Protein Evolution: Understanding the Patterns of Evolutionary Sequence Divergence.Annual review of biophysics · 2017Review
- Identification of positive selection in genes is greatly improved by using experimentally informed site-specific models.Biology direct · 2017Article
- Sequence amplification via cell passaging creates spurious signals of positive adaptation in influenza virus H3N2 hemagglutinin.Virus evolution · 2016Article
- Detection and sequence/structure mapping of biophysical constraints to protein variation in saturated mutational libraries and protein sequence alignments with a dedicated server.BMC bioinformatics · 2016Article
- Dissecting the roles of local packing density and longer-range effects in protein sequence evolution.Proteins · 2016Article
- Functional Divergence in Teleost Cardiac Troponin Paralogs Guides Variation in the Interaction of TnI Switch Region with TnC.Genome biology and evolution · 2016Article
- Causes of evolutionary rate variation among protein sites.Nature reviews. Genetics · 2016Review
- Determination of antigenicity-altering patches on the major surface protein of human influenza A/H3N2 viruses.Virus evolution · 2016Article
- The utility of protein structure as a predictor of site-wise dN/dS varies widely among HIV-1 proteins.Journal of the Royal Society, Interface · 2015Article
- Functional Constraint Profiling of a Viral Protein Reveals Discordance of Evolutionary Conservation and Functionality.PLoS genetics · 2015Article
- Geometric Constraints Dominate the Antigenic Evolution of Influenza H3N2 Hemagglutinin.PLoS pathogens · 2015Article
- The relationship between dN/dS and scaled selection coefficients.Molecular biology and evolution · 2015Article
- How structural and physicochemical determinants shape sequence constraints in a functional enzyme.PloS one · 2015Article
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2 authors.
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Abstract
We present a novel method to identify sites under selection in protein-coding genes. Our method combines the traditional Goldman-Yang model of coding-sequence evolution with the information obtained from the 3D structure of the evolving protein, specifically the relative solvent accessibility (RSA) of individual residues. We develop a random-effects likelihood sites model in which rate classes are RSA dependent. The RSA dependence is modeled with linear functions. We demonstrate that our RSA-dependent model provides a significantly better fit to molecular sequence data than does a traditional, RSA-independent model. We further show that our model provides a natural, RSA-dependent neutral baseline for the evolutionary rate ratio ω = dN/dS Sites that deviate from this neutral baseline likely experience selection pressure for function. We apply our method to the influenza proteins hemagglutinin and neuraminidase. For hemagglutinin, our method recovers positively selected sites near the sialic acid-binding site and negatively selected sites that may be important for trimerization. For neuraminidase, our method recovers the oseltamivir resistance site and otherwise suggests that few sites deviate from the neutral baseline. Our method is broadly applicable to any protein sequences for which structural data are available or can be obtained via homology modeling or threading.
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