Emerging methods in protein co-evolution (Q38086348)

28 August 2017

Emerging methods in protein co-evolution (English)

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28 August 2017

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3

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28 August 2017

David de Juan

1

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PubMed ID

23458856

28 August 2017

Florencio Pazos

series ordinal

2

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28 August 2017

5 March 2013

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28 August 2017

Nature Reviews Genetics

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28 August 2017

14

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28 August 2017

4

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28 August 2017

249-261

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https://scigraph.springernature.com/pub.10.1038/nrg3414

28 August 2017

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cites work

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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31 March 2020

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

31 March 2020

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Compensating changes in protein multiple sequence alignments

31 March 2020

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How frequent are correlated changes in families of protein sequences?

31 March 2020

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31 March 2020

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Scoring docking models with evolutionary information.

31 March 2020

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Detecting coevolution in and among protein domains

31 March 2020

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

31 March 2020

1 reference

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

31 March 2020

1 reference

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

31 March 2020

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

31 March 2020

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A method to predict functional residues in proteins

31 March 2020

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An evolutionary trace method defines binding surfaces common to protein families

31 March 2020

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Co-evolution of proteins with their interaction partners

31 March 2020

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31 March 2020

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The coevolution of gene family trees

31 March 2020

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Covariation of mutations in the V3 loop of human immunodeficiency virus type 1 envelope protein: an information theoretic analysis

31 March 2020

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

31 March 2020

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

31 March 2020

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

31 March 2020

1 reference

A novel method for detecting intramolecular coevolution: adding a further dimension to selective constraints analyses.

31 March 2020

1 reference

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

31 March 2020

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

31 March 2020

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

31 March 2020

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

31 March 2020

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31 March 2020

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An evolutionarily conserved network of amino acids mediates gating in voltage-dependent potassium channels

31 March 2020

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A model-based approach for detecting coevolving positions in a molecule.

31 March 2020

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Coevolving protein residues: maximum likelihood identification and relationship to structure.

31 March 2020

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

31 March 2020

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

31 March 2020

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

31 March 2020

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Learning generative models for protein fold families.

31 March 2020

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Disentangling direct from indirect co-evolution of residues in protein alignments

31 March 2020

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31 March 2020

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Deep architectures for protein contact map prediction

31 March 2020

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Co-evolution and co-adaptation in protein networks

31 March 2020

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Protein co-evolution, co-adaptation and interactions

31 March 2020

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

31 March 2020

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Automatic methods for predicting functionally important residues

31 March 2020

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

31 March 2020

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

31 March 2020

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Evolutionary information for specifying a protein fold

31 March 2020

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Evolutionarily conserved pathways of energetic connectivity in protein families

31 March 2020

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

31 March 2020

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Evolutionarily conserved networks of residues mediate allosteric communication in proteins

31 March 2020

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Hot spots for allosteric regulation on protein surfaces

31 March 2020

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

31 March 2020

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A family of evolution-entropy hybrid methods for ranking protein residues by importance.

31 March 2020

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Using orthologous and paralogous proteins to identify specificity-determining residues in bacterial transcription factors.

31 March 2020

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Combining specificity determining and conserved residues improves functional site prediction

31 March 2020

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Three-dimensional cluster analysis identifies interfaces and functional residue clusters in proteins

31 March 2020

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Determinants of protein function revealed by combinatorial entropy optimization

31 March 2020

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

31 March 2020

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Protein sectors: evolutionary units of three-dimensional structure

31 March 2020

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Validation of coevolving residue algorithms via pipeline sensitivity analysis: ELSC and OMES and ZNMI, oh my!

31 March 2020

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Predicting biological networks from genomic data

31 March 2020

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Challenges for the prediction of macromolecular interactions

31 March 2020

1 reference

STRING: a database of predicted functional associations between proteins

31 March 2020

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Assessing protein co-evolution in the context of the tree of life assists in the prediction of the interactome.

31 March 2020

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

31 March 2020

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Predicting protein domain interactions from coevolution of conserved regions

31 March 2020

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

31 March 2020

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

31 March 2020

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Selection of organisms for the co-evolution-based study of protein interactions

31 March 2020

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Comparison of phylogenetic trees through alignment of embedded evolutionary distances

31 March 2020

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The human protein coevolution network.

31 March 2020

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Exploiting the co-evolution of interacting proteins to discover interaction specificity

31 March 2020

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Predicting protein-protein interaction by searching evolutionary tree automorphism space

31 March 2020

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

31 March 2020

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Co-evolutionary analysis of domains in interacting proteins reveals insights into domain-domain interactions mediating protein-protein interactions

31 March 2020

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31 March 2020

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Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles

31 March 2020

1 reference

Microbial genescapes: phyletic and functional patterns of ORF distribution among prokaryotes

31 March 2020

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

31 March 2020

1 reference

Predicting protein function with hierarchical phylogenetic profiles: the Gene3D Phylo-Tuner method applied to eukaryotic genomes

31 March 2020

1 reference

Inferring functional linkages between proteins from evolutionary scenarios

31 March 2020

1 reference

A novel method for assigning functional linkages to proteins using enhanced phylogenetic trees.

31 March 2020

1 reference

Refined phylogenetic profiles method for predicting protein-protein interactions.

31 March 2020

1 reference

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

31 March 2020

1 reference

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

31 March 2020

1 reference

Codep: maximizing co-evolutionary interdependencies to discover interacting proteins

31 March 2020

1 reference

The coevolving web of life

31 March 2020

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CASP6 assessment of contact prediction.

31 March 2020

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Direct correlation analysis improves fold recognition

31 March 2020

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Protein 3D structure computed from evolutionary sequence variation

31 March 2020

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Three-dimensional structures of membrane proteins from genomic sequencing

31 March 2020

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

31 March 2020

1 reference

Genomics-aided structure prediction

31 March 2020

1 reference

Characterization of pathogenic germline mutations in human protein kinases

31 March 2020

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Prioritization of pathogenic mutations in the protein kinase superfamily

31 March 2020

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Effector recognition by the small GTP-binding proteins Ras and Ral

31 March 2020

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Identification of conserved amino acid residues in rat liver carnitine palmitoyltransferase I critical for malonyl-CoA inhibition. Mutation of methionine 593 abolishes malonyl-CoA inhibition

31 March 2020

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Identification of amino acid residues crucial for chemokine receptor dimerization.

31 March 2020

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beta-arrestin-dependent, G protein-independent ERK1/2 activation by the beta2 adrenergic receptor

31 March 2020

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

31 March 2020

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

31 March 2020

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Adaptive mutations that prevent crosstalk enable the expansion of paralogous signaling protein families

31 March 2020

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Coevolution predicts direct interactions between mtDNA-encoded and nDNA-encoded subunits of oxidative phosphorylation complex i

31 March 2020

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

31 March 2020

1 reference

Peroxiredoxins are conserved markers of circadian rhythms

31 March 2020

1 reference

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

31 March 2020

1 reference

Coevolution of interacting fertilization proteins

31 March 2020

1 reference

Genetics of natural populations. XIX. Origin of heterosis through natural selection in populations of Drosophila pseudoobscura

31 March 2020

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23458856

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

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

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23458856

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1038/NRG3414

1 reference

PubMed ID

23458856

Dimensions Publication ID

28 August 2017

0 references

1 reference

PubMed ID

23458856