ArticleProtein science : a publication of the Protein Society2016
The tangled bank of amino acids.
Article in Protein science : a publication of the Protein Society, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- A Natural qE- and qZ-Deficient Alga Retains Functional Plant-Like and Chlorophycean Violaxanthin De-Epoxidases.bioRxiv : the preprint server for biology · 2026Article
- Unraveling the genomic structures, conserved functional domains and evolutionary dynamics of beta-defensins in Bubalus bubalis and Ovis aries.Immunogenetics · 2026Article
- Accurate prediction of substitution rates at protein sites with a mutation-selection model.Scientific reports · 2025Article
- Substitution Models of Protein Evolution with Selection on Enzymatic Activity.Molecular biology and evolution · 2024Article
- Article
- Evolution of Amino Acid Propensities under Stability-Mediated Epistasis.Molecular biology and evolution · 2022Article
- An Improved Codon Modeling Approach for Accurate Estimation of the Mutation Bias.Molecular biology and evolution · 2022Article
- Hotspots for mutations in the SARS-CoV-2 spike glycoprotein: a correspondence analysis.Scientific reports · 2021Article
- Inferring Long-Term Effective Population Size with Mutation-Selection Models.Molecular biology and evolution · 2021Article
- Navigating the amino acid sequence space between functional proteins using a deep learning framework.PeerJ. Computer science · 2021Article
- A Phylogenetic Rate Parameter Indicates Different Sequence Divergence Patterns in Orthologs and Paralogs.Journal of molecular evolution · 2020Article
- Site-Specific Amino Acid Distributions Follow a Universal Shape.Journal of molecular evolution · 2020Article
- Co-evolution in the Jungle: From Leafcutter Ant Colonies to Chromosomal Ends.Journal of molecular evolution · 2020Review
- Evaluating Statistical Multiple Sequence Alignment in Comparison to Other Alignment Methods on Protein Data Sets.Systematic biology · 2019Article
- Relative Evolutionary Rates in Proteins Are Largely Insensitive to the Substitution Model.Molecular biology and evolution · 2018Article
- Article
- Beyond Thermodynamic Constraints: Evolutionary Sampling Generates Realistic Protein Sequence Variation.Genetics · 2018Article
- Protein evolution depends on multiple distinct population size parameters.BMC evolutionary biology · 2018Review
- Sequence entropy of folding and the absolute rate of amino acid substitutions.Nature ecology & evolution · 2017Article
- Biophysical Models of Protein Evolution: Understanding the Patterns of Evolutionary Sequence Divergence.Annual review of biophysics · 2017Review
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2 authors.
Funding
Abstract
The use of amino acid substitution matrices to model protein evolution has yielded important insights into both the evolutionary process and the properties of specific protein families. In order to make these models tractable, standard substitution matrices represent the average results of the evolutionary process rather than the underlying molecular biophysics and population genetics, treating proteins as a set of independently evolving sites rather than as an integrated biomolecular entity. With advances in computing and the increasing availability of sequence data, we now have an opportunity to move beyond current substitution matrices to more interpretable mechanistic models with greater fidelity to the evolutionary process of mutation and selection and the holistic nature of the selective constraints. As part of this endeavour, we consider how epistatic interactions induce spatial and temporal rate heterogeneity, and demonstrate how these generally ignored factors can reconcile standard substitution rate matrices and the underlying biology, allowing us to better understand the meaning of these substitution rates. Using computational simulations of protein evolution, we can demonstrate the importance of both spatial and temporal heterogeneity in modelling protein evolution.
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