Emerging methods in protein co-evolution

BUTTERFLIES AND PLANTS: A STUDY IN COEVOLUTION

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STRING: a database of predicted functional associations between proteins

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The Coevolutionary Process

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Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles

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Direct-coupling analysis of residue coevolution captures native contacts across many protein families

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Evolutionarily Conserved Pathways of Energetic Connectivity in Protein Families

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An Evolutionary Trace Method Defines Binding Surfaces Common to Protein Families

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Protein 3D Structure Computed from Evolutionary Sequence Variation

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Identification of direct residue contacts in protein–protein interaction by message passing

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Peroxiredoxins are conserved markers of circadian rhythms

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Correlated mutations and residue contacts in proteins

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Evolutionarily conserved networks of residues mediate allosteric communication in proteins

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PSICOV: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments

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β-Arrestin-dependent, G Protein-independent ERK1/2 Activation by the β2 Adrenergic Receptor

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Protein Sectors: Evolutionary Units of Three-Dimensional Structure

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Similarity of phylogenetic trees as indicator of protein–protein interaction

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Three-Dimensional Structures of Membrane Proteins from Genomic Sequencing

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Correlated mutations contain information about protein-protein interaction 1 1Edited by A. R. Fersht

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Mutual information without the influence of phylogeny or entropy dramatically improves residue contact prediction

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An improved method for determining codon variability in a gene and its application to the rate of fixation of mutations in evolution

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Co-evolution of proteins with their interaction partners 1 1Edited by B. Honig

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Evolutionary information for specifying a protein fold

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A method to predict functional residues in proteins

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Hot Spots for Allosteric Regulation on Protein Surfaces

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Learning generative models for protein fold families

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GENETICS OF NATURAL POPULATIONS. XIX. ORIGIN OF HETEROSIS THROUGH NATURAL SELECTION IN POPULATIONS OF DROSOPHILA PSEUDOOBSCURA

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Determinants of protein function revealed by combinatorial entropy optimization

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Can three-dimensional contacts in protein structures be predicted by analysis of correlated mutations?

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A Family of Evolution–Entropy Hybrid Methods for Ranking Protein Residues by Importance

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Correlation of co-ordinated amino acid substitutions with function in viruses related to tobacco mosaic virus

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Deep architectures for protein contact map prediction

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Using information theory to search for co-evolving residues in proteins

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Covariation of mutations in the v3 loop of human immunodeficiency virus type 1 envelope protein: an information theoretic analysis

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Analysis and prediction of functional sub-types from protein sequence alignments

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In silico two‐hybrid system for the selection of physically interacting protein pairs

Pazos, F., & Valencia, A. (2002) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.10074 · Cited by 243 · see citing works

How frequent are correlated changes in families of protein sequences?

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Coevolving protein residues: maximum likelihood identification and relationship to structure 1 1Edited by G. Von Heijne

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Influence of conservation on calculations of amino acid covariance in multiple sequence alignments

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Three-dimensional cluster analysis identifies interfaces and functional residue clusters in proteins11Edited by J. Thornton

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Discovery of uncharacterized cellular systems by genome-wide analysis of functional linkages

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Genomics-aided structure prediction

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Exploiting the Co-evolution of Interacting Proteins to Discover Interaction Specificity

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Improving contact predictions by the combination of correlated mutations and other sources of sequence information

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Automatic Methods for Predicting Functionally Important Residues

Mesa, A. D. S., Pazos, F., & Valencia, A. (2003) · Journal of Molecular Biology · doi:10.1016/s0022-2836(02)01451-1 · Cited by 204 · see citing works

Structural clusters of evolutionary trace residues are statistically significant and common in proteins

Madabushi, S., Yao, H., Marsh, M., Kristensen, D. M., Philippi, A., Sowa, M. E., & Lichtarge, O. (2002) · Journal of Molecular Biology · doi:10.1006/jmbi.2001.5327 · Cited by 200 · see citing works

Disentangling Direct from Indirect Co-Evolution of Residues in Protein Alignments

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High-confidence prediction of global interactomes based on genome-wide coevolutionary networks

Juan, D., Pazos, F., & Valencia, A. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0709671105 · Cited by 193 · see citing works

Protein co‐evolution, co‐adaptation and interactions

Pazos, F., & Valencia, A. (2008) · The EMBO Journal · doi:10.1038/emboj.2008.189 · Cited by 191 · see citing works

Accurate prediction of protein–protein interactions from sequence alignments using a Bayesian method

Burger, L., & van Nimwegen, E. (2008) · Molecular Systems Biology · doi:10.1038/msb4100203 · Cited by 191 · see citing works

Identification of amino acid residues crucial for chemokine receptor dimerization

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The coevolution of gene family trees

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Mapping pathways of allosteric communication in GroEL by analysis of correlated mutations

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Accurate de novo structure prediction of large transmembrane protein domains using fragment-assembly and correlated mutation analysis

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A Novel Method for Detecting Intramolecular Coevolution: Adding a Further Dimension to Selective Constraints Analyses

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The Coevolving Web of Life(American Society of Naturalists Presidential Address)

Thompson, J. N. (2009) · The American Naturalist · doi:10.1086/595752 · Cited by 165 · see citing works

Detecting Coevolution in and among Protein Domains

Yeang, C., & Haussler, D. H. (2007) · PLoS Computational Biology · doi:10.1371/journal.pcbi.0030211 · Cited by 165 · see citing works

Predicting Functional Gene Links from Phylogenetic-Statistical Analyses of Whole Genomes

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High-resolution protein complexes from integrating genomic information with molecular simulation

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Compensating changes in protein multiple sequence alignments

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Predicting functional gene-links from phylogenetic-statistical analyses of whole genomes

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Assessing Protein Co-evolution in the Context of the Tree of Life Assists in the Prediction of the Interactome

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A Model-Based Approach for Detecting Coevolving Positions in a Molecule

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Protein interactions and ligand binding: From protein subfamilies to functional specificity

Rausell, A., Juan, D., Pazos, F., & Valencia, A. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0908044107 · Cited by 145 · see citing works

Coevolution of Interacting Fertilization Proteins

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The inference of protein-protein interactions by co-evolutionary analysis is improved by excluding the information about the phylogenetic relationships

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Structural basis of histidine kinase autophosphorylation deduced by integrating genomics, molecular dynamics, and mutagenesis

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Using Orthologous and Paralogous Proteins to Identify Specificity-determining Residues in Bacterial Transcription Factors

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Co-evolutionary Analysis of Domains in Interacting Proteins Reveals Insights into Domain–Domain Interactions Mediating Protein–Protein Interactions

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Adaptive Mutations that Prevent Crosstalk Enable the Expansion of Paralogous Signaling Protein Families

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Using multiple interdependency to separate functional from phylogenetic correlations in protein alignments

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Microbial Genescapes: Phyletic and Functional Patterns of ORF Distribution among Prokaryotes

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Correlated mutations in models of protein sequences: phylogenetic and structural effects

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Refined phylogenetic profiles method for predicting protein-protein interactions

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Highly divergent sequences of the pollen self‐incompatibility ( S ) gene in class‐I S haplotypes of Brassica campestris (syn. rapa ) L

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Distinct faces of the Ku heterodimer mediate DNA repair and telomeric functions

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Genetic Architecture of Physiological Phenotypes: Empirical Evidence for Coadapted Gene Complexes

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Evolution-guided discovery and recoding of allosteric pathway specificity determinants in psychoactive bioamine receptors

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Crystal Structures of the Outer Membrane Domain of Intimin and Invasin from Enterohemorrhagic E. coli and Enteropathogenic Y. pseudotuberculosis

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CASP6 assessment of contact prediction

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Challenges for the prediction of macromolecular interactions

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Effector Recognition by the Small GTP-binding Proteins Ras and Ral

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Studying the co-evolution of protein families with the Mirrortree web server

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On Coadaptation in Drosophila

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Discovering functional linkages and uncharacterized cellular pathways using phylogenetic profile comparisons: a comprehensive assessment

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Predicting protein-protein interaction by searching evolutionary tree automorphism space

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Identification of Conserved Amino Acid Residues in Rat Liver Carnitine Palmitoyltransferase I Critical for Malonyl-CoA Inhibition

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Coevolution Predicts Direct Interactions between mtDNA-Encoded and nDNA-Encoded Subunits of Oxidative Phosphorylation Complex I

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The human protein coevolution networkPreprint

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An Evolutionarily Conserved Network of Amino Acids Mediates Gating in Voltage-dependent Potassium Channels

Fleishman, S. J., Yifrach, O., & Ben‐Tal, N. (2004) · Journal of Molecular Biology · doi:10.1016/j.jmb.2004.04.064 · Cited by 59 · see citing works

Partial correlation coefficient between distance matrices as a new indicator of protein–protein interactions

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Correlated Evolution of Interacting Proteins: Looking Behind the Mirrortree

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Predicting Protein Function with Hierarchical Phylogenetic Profiles: The Gene3D Phylo-Tuner Method Applied to Eukaryotic Genomes

Ranea, J. A. G., Yeats, C., Grant, A., & Orengo, C. A. (2007) · PLoS Computational Biology · doi:10.1371/journal.pcbi.0030237 · Cited by 48 · see citing works

Predicting biological networks from genomic data

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Predicting protein domain interactions from coevolution of conserved regions

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Bayesian search of functionally divergent protein subgroups and their function specific residues

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Scoring docking models with evolutionary information

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Tight coevolution of proliferating cell nuclear antigen (PCNA)-partner interaction networks in fungi leads to interspecies network incompatibility

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Co‐evolution and co‐adaptation in protein networks

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Combining specificity determining and conserved residues improves functional site prediction

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Predicted residue–residue contacts can help the scoring of 3D models

Tress, M. L., & Valencia, A. (2010) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.22714 · Cited by 39 · see citing works

Codep: Maximizing co‐evolutionary interdependencies to discover interacting proteins

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Validation of Coevolving Residue Algorithms via Pipeline Sensitivity Analysis: ELSC and OMES and ZNMI, Oh My!

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Inferring Functional Linkages between Proteins from Evolutionary Scenarios

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Enhancing the prediction of protein pairings between interacting families using orthology information

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Prioritization of pathogenic mutations in the protein kinase superfamily

Izarzugaza, J. M. G., del Pozo, Á., Vázquez, M., & Valencia, A. (2012) · BMC Genomics · doi:10.1186/1471-2164-13-s4-s3 · Cited by 24 · see citing works

Comparison of phylogenetic trees through alignment of embedded evolutionary distances

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AlphaFold and Implications for Intrinsically Disordered Proteins

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Sequence co-evolution gives 3D contacts and structures of protein complexes

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Learning the protein language: Evolution, structure, and function

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Distance-based protein folding powered by deep learning

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Systematic identification of conditionally folded intrinsically disordered regions by AlphaFold2

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Predicting functional effect of missense variants using graph attention neural networks

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Inter-residue, inter-protein and inter-family coevolution: bridging the scales

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Protein structure prediction by <i>AlphaFold</i> 2: are attention and symmetries all you need?

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CyToStruct: augmenting the network visualization of cytoscape with the power of molecular viewers

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Deep learning reveals many more inter-protein residue-residue contacts than direct coupling analysis

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A Model of Substitution Trajectories in Sequence Space and Long-Term Protein Evolution

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