ArticleJournal of molecular evolution2013
Unearthing the root of amino acid similarity.
Article in Journal of molecular evolution, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Quantitative analysis of trafficking defects induced by heterozygous expression of hERG voltage sensor domain variants.Channels (Austin, Tex.) · 2026Article
- Towards whole plastome phylogeography: resolving small genetic distances among European Arnica montana L. with the PlastidPipeline.Scientific reports · 2026Article
- RNA exosome component EXOSC10 variants identified in a patient with premature ovarian insufficiency†.Biology of reproduction · 2026Article
- Candida albicans' inorganic phosphate transport and evolutionary adaptation to phosphate scarcity.PLoS genetics · 2024Article
- Computational identification of antibody-binding epitopes from mimotope datasets.Frontiers in bioinformatics · 2024Article
- Interpretable Machine Learning of Amino Acid Patterns in Proteins: A Statistical Ensemble Approach.Journal of chemical theory and computation · 2023Article
- General Theory of Specific Binding: Insights from a Genetic-Mechano-Chemical Protein Model.Molecular biology and evolution · 2022Article
- Research progress of reduced amino acid alphabets in protein analysis and prediction.Computational and structural biotechnology journal · 2022Review
- Evolution as a Guide to DesigningInternational journal of molecular sciences · 2021Review
- Divergent Evolution of a Protein-Protein Interaction Revealed through Ancestral Sequence Reconstruction and Resurrection.Molecular biology and evolution · 2021Article
- The Ancient Operational Code is Embedded in the Amino Acid Substitution Matrix and aaRS Phylogenies.Journal of molecular evolution · 2020Article
- dagLogo: An R/Bioconductor package for identifying and visualizing differential amino acid group usage in proteomics data.PloS one · 2020Article
- Experimental solutions to problems defining the origin of codon-directed protein synthesis.Bio Systems · 2019Review
- Adaptive Properties of the Genetically Encoded Amino Acid Alphabet Are Inherited from Its Subsets.Scientific reports · 2019Article
- RAACBook: a web server of reduced amino acid alphabet for sequence-dependent inference by using Chou's five-step rule.Database : the journal of biological databases and curation · 2019Article
- Environmental Adaptation from the Origin of Life to the Last Universal Common Ancestor.Origins of life and evolution of the biosphere : the journal of the International Society for the Study of the Origin of Life · 2018Article
- Amyloidogenic motifs revealed by n-gram analysis.Scientific reports · 2017Article
- Extraordinarily adaptive properties of the genetically encoded amino acids.Scientific reports · 2015Article
- The origin of the genetic code: matter of metabolism or physicochemical determinism?Journal of molecular evolution · 2013Article
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Similarities and differences between amino acids define the rates at which they substitute for one another within protein sequences and the patterns by which these sequences form protein structures. However, there exist many ways to measure similarity, whether one considers the molecular attributes of individual amino acids, the roles that they play within proteins, or some nuanced contribution of each. One popular approach to representing these relationships is to divide the 20 amino acids of the standard genetic code into groups, thereby forming a simplified amino acid alphabet. Here, we develop a method to compare or combine different simplified alphabets, and apply it to 34 simplified alphabets from the scientific literature. We use this method to show that while different suggestions vary and agree in non-intuitive ways, they combine to reveal a consensus view of amino acid similarity that is clearly rooted in physico-chemistry.
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