ArticlePLoS computational biology2007
Detecting coevolution in and among protein domains.
Article in PLoS computational biology, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 92 papers.
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92 citing papers in PubMed, 172 citations in OpenAlex.
- Exploring cooperation among social pathogens: a computational perspective.FEMS microbiology reviews · 2026Review
- Protein Structural Phylogenetics.Genome biology and evolution · 2025Review
- Identification of coevolving positions by ancestral reconstruction.Communications biology · 2025Article
- CastNet: a systems-level sequence evolution simulator.BMC bioinformatics · 2023Article
- A Novel Information-Theory-Based Genetic Distance That Approximates Phenotypic Differences.Journal of computational biology : a journal of computational molecular cell biology · 2023Article
- Mutual information networks reveal evolutionary relationships within the influenza A virus polymerase.bioRxiv : the preprint server for biology · 2023Article
- Mutual information networks reveal evolutionary relationships within the influenza A virus polymerase.Virus evolution · 2023Article
- Local fitness and epistatic effects lead to distinct patterns of linkage disequilibrium in protein-coding genes.Genetics · 2022Article
- Modulating Glycoside Hydrolase Activity between Hydrolysis and Transfer Reactions Using an Evolutionary Approach.Molecules (Basel, Switzerland) · 2021Article
- Evolutionary conservation of RNA sequence and structure.Wiley interdisciplinary reviews. RNA · 2021Review
- Structural Insights into Carboxylic Polyester-Degrading Enzymes and Their Functional Depolymerizing Neighbors.International journal of molecular sciences · 2021Article
- Inter-protein residue covariation information unravels physically interacting protein dimers.BMC bioinformatics · 2020Article
- Directional auxin fluxes in plants by intramolecular domain-domain coevolution of PIN auxin transporters.The New phytologist · 2020Article
- Simultaneous Bayesian inference of phylogeny and molecular coevolution.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- CoevDB: a database of intramolecular coevolution among protein-coding genes of the bony vertebrates.Nucleic acids research · 2019Article
- Characterizing human genomic coevolution in locus-gene regulatory interactions.BioData mining · 2019Article
- DeepCDpred: Inter-residue distance and contact prediction for improved prediction of protein structure.PloS one · 2019Article
- Article
- Network Analysis of RAD51 Proteins in Metazoa and the Evolutionary Relationships With Their Archaeal Homologs.Frontiers in genetics · 2018Article
- Widespread evolutionary crosstalk among protein domains in the context of multi-domain proteins.PloS one · 2018Article
32 more citing papers are in PubMed but not listed here.
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2 authors at 2 institutions in 1 country.
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No grant is acknowledged in the PubMed record.
Abstract
Correlated changes of nucleic or amino acids have provided strong information about the structures and interactions of molecules. Despite the rich literature in coevolutionary sequence analysis, previous methods often have to trade off between generality, simplicity, phylogenetic information, and specific knowledge about interactions. Furthermore, despite the evidence of coevolution in selected protein families, a comprehensive screening of coevolution among all protein domains is still lacking. We propose an augmented continuous-time Markov process model for sequence coevolution. The model can handle different types of interactions, incorporate phylogenetic information and sequence substitution, has only one extra free parameter, and requires no knowledge about interaction rules. We employ this model to large-scale screenings on the entire protein domain database (Pfam). Strikingly, with 0.1 trillion tests executed, the majority of the inferred coevolving protein domains are functionally related, and the coevolving amino acid residues are spatially coupled. Moreover, many of the coevolving positions are located at functionally important sites of proteins/protein complexes, such as the subunit linkers of superoxide dismutase, the tRNA binding sites of ribosomes, the DNA binding region of RNA polymerase, and the active and ligand binding sites of various enzymes. The results suggest sequence coevolution manifests structural and functional constraints of proteins. The intricate relations between sequence coevolution and various selective constraints are worth pursuing at a deeper level.
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