ArticleBMC evolutionary biology2007
Detecting groups of coevolving positions in a molecule: a clustering approach.
Article in BMC evolutionary biology, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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27 citing papers in PubMed, 59 citations in OpenAlex.
- Developing and Applying RNA Empirical Models With Secondary Structure Insights for Orthoptera Phylogenetics.Ecology and evolution · 2025Article
- PHACE: Phylogeny-Aware Detection of Molecular Coevolution.Molecular biology and evolution · 2025Article
- Comparative Analysis of Drosophila Bam and Bgcn Sequences and Predicted Protein Structural Evolution.Journal of molecular evolution · 2025Article
- Article
- Network of epistatic interactions in an enzyme active site revealed by large-scale deep mutational scanning.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- The Structural Determinants of Intra-Protein Compensatory Substitutions.Molecular biology and evolution · 2022Article
- Selection on the Major Color Gene Melanocortin-1-Receptor Shaped the Evolution of the Melanocortin System Genes.International journal of molecular sciences · 2017Article
- Unraveling the evolution and coevolution of small regulatory RNAs and coding genes in Listeria.BMC genomics · 2017Article
- Coevolution analysis of Hepatitis C virus genome to identify the structural and functional dependency network of viral proteins.Scientific reports · 2016Article
- Covariation Is a Poor Measure of Molecular Coevolution.Molecular biology and evolution · 2015Article
- Coevolutionary analyses require phylogenetically deep alignments and better null models to accurately detect inter-protein contacts within and between species.BMC bioinformatics · 2015Article
- Coordinated rates of evolution between interacting plastid and nuclear genes in Geraniaceae.The Plant cell · 2015Article
- A new ensemble coevolution system for detecting HIV-1 protein coevolution.Biology direct · 2015Article
- Defining structural and evolutionary modules in proteins: a community detection approach to explore sub-domain architecture.BMC structural biology · 2013Article
- Prediction of contact residue pairs based on co-substitution between sites in protein structures.PloS one · 2013Article
- Improving the thermostability of alpha-amylase by combinatorial coevolving-site saturation mutagenesis.BMC bioinformatics · 2012Article
- Accelerated evolution and coevolution drove the evolutionary history of AGPase sub-units during angiosperm radiation.Annals of botany · 2012Article
- Article
- Integrated analysis of residue coevolution and protein structure in ABC transporters.PloS one · 2012Article
- Fast and robust characterization of time-heterogeneous sequence evolutionary processes using substitution mapping.PloS one · 2012Article
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Authors and funding
2 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundAlthough the patterns of co-substitutions in RNA is now well characterized, detection of coevolving positions in proteins remains a difficult task. It has been recognized that the signal is typically weak, due to the fact that (i) amino-acid are characterized by various biochemical properties, so that distinct amino acids changes are not functionally equivalent, and (ii) a given mutation can be compensated by more than one mutation, at more than one position.
resultsWe present a new method based on phylogenetic substitution mapping. The two above-mentioned problems are addressed by (i) the introduction of a weighted mapping, which accounts for the biochemical effects (volume, polarity, charge) of amino-acid changes, (ii) the use of a clustering approach to detect groups of coevolving sites of virtually any size, and (iii) the distinction between biochemical compensation and other coevolutionary mechanisms. We apply this methodology to a previously studied data set of bacterial ribosomal RNA, and to three protein data sets (myoglobin of vertebrates, S-locus Receptor Kinase and Methionine Amino-Peptidase).
conclusionWe succeed in detecting groups of sites which significantly depart the null hypothesis of independence. Group sizes range from pairs to groups of size approximately 10, depending on the substitution weights used. The structural and functional relevance of these groups of sites are assessed, and the various evolutionary processes potentially generating correlated substitution patterns are discussed.
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