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Co-evolution techniques are reshaping the way we do structural bioinformatics

https://doi.org/10.12688/f1000research.11543.1
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/pro.5560040113openalex-snapshot
A procedure for detecting structural domains in proteins
inferredcites →https://doi.org/10.1002/pro.5560040507openalex-snapshot
Continuous and discontinuous domains: An algorithm for the automatic generation of reliable protein domain definitions
inferredcites →https://doi.org/10.1002/prot.10198openalex-snapshot
Information‐theoretic dissection of pairwise contact potentials
inferredcites →https://doi.org/10.1002/prot.1173openalex-snapshot
Progress in predicting inter-residue contacts of proteins with neural networks and correlated mutations
inferredcites →https://doi.org/10.1002/prot.21791openalex-snapshot
Contact prediction using mutual information and neural nets
inferredcites →https://doi.org/10.1002/prot.22934openalex-snapshot
Learning generative models for protein fold families
inferredcites →https://doi.org/10.1002/prot.24181openalex-snapshot
Prediction of protein domain boundaries from inverse covariances
inferredcites →https://doi.org/10.1002/prot.24974openalex-snapshot
Improved de novo structure prediction in CASP 11 by incorporating coevolution information into Rosetta
inferredcites →https://doi.org/10.1002/prot.24979openalex-snapshot
COMSAT: Residue contact prediction of transmembrane proteins based on support vector machines and mixed integer linear programming
inferredcites →https://doi.org/10.1002/prot.25064openalex-snapshot
Critical assessment of methods of protein structure prediction: Progress and new directions in round XI
inferredcites →https://doi.org/10.1002/prot.25180openalex-snapshot
Lessons from (co‐)evolution in the docking of proteins and peptides for CAPRI Rounds 28–35
inferredcites →https://doi.org/10.1002/prot.25292openalex-snapshot
Coevolutionary constraints in the sequence‐space of macromolecular complexes reflect their self‐assembly pathways
inferredcites →https://doi.org/10.1002/prot.340180402openalex-snapshot
Correlated mutations and residue contacts in proteins
inferredcites →https://doi.org/10.1007/s10295-016-1811-1openalex-snapshot
Correlated positions in protein evolution and engineering
inferredcites →https://doi.org/10.1016/j.cell.2012.04.012openalex-snapshot
Three-Dimensional Structures of Membrane Proteins from Genomic Sequencing
inferredcites →https://doi.org/10.1016/j.cell.2016.09.010openalex-snapshot
Structured States of Disordered Proteins from Genomic Sequences
inferredcites →https://doi.org/10.1016/j.str.2015.10.025openalex-snapshot
Residues Coevolution Guides the Systematic Identification of Alternative Functional Conformations in Proteins
inferredcites →https://doi.org/10.1016/s1359-0278(97)00060-6openalex-snapshot
Improving contact predictions by the combination of correlated mutations and other sources of sequence information
inferredcites →https://doi.org/10.1021/acs.jpcb.6b11976openalex-snapshot
Evolutionary Covariance Combined with Molecular Dynamics Predicts a Framework for Allostery in the MutS DNA Mismatch Repair Protein
inferredcites →https://doi.org/10.1038/nbt.2419openalex-snapshot
Protein structure prediction from sequence variation
inferredcites →https://doi.org/10.1038/nbt.3769openalex-snapshot
Mutation effects predicted from sequence co-variation
inferredcites →https://doi.org/10.1038/srep13652openalex-snapshot
Dimeric interactions and complex formation using direct coevolutionary couplings
inferredcites →https://doi.org/10.1039/c3cp55275fopenalex-snapshot
From structure to function: the convergence of structure based models and co-evolutionary information
inferredcites →https://doi.org/10.1073/pnas.1111471108openalex-snapshot
Direct-coupling analysis of residue coevolution captures native contacts across many protein families
inferredcites →https://doi.org/10.1073/pnas.1120036109openalex-snapshot
Accurate de novo structure prediction of large transmembrane protein domains using fragment-assembly and correlated mutation analysis
inferredcites →https://doi.org/10.1073/pnas.1314045110openalex-snapshot
Assessing the utility of coevolution-based residue–residue contact predictions in a sequence- and structure-rich era
inferredcites →https://doi.org/10.1073/pnas.1315625110openalex-snapshot
Coevolutionary signals across protein lineages help capture multiple protein conformations
inferredcites →https://doi.org/10.1073/pnas.1508584112openalex-snapshot
From residue coevolution to protein conformational ensembles and functional dynamics
inferredcites →https://doi.org/10.1073/pnas.1606762113openalex-snapshot
Inferring interaction partners from protein sequences
inferredcites →https://doi.org/10.1073/pnas.1607570113openalex-snapshot
Simultaneous identification of specifically interacting paralogs and interprotein contacts by direct coupling analysis
inferredcites →https://doi.org/10.1089/cmb.2015.0236openalex-snapshot
OMPcontact: An Outer Membrane Protein Inter-Barrel Residue Contact Prediction Method
inferredcites →https://doi.org/10.1093/bib/bbm052openalex-snapshot
Correlated substitution analysis and the prediction of amino acid structural contacts
inferredcites →https://doi.org/10.1093/bioinformatics/btr638openalex-snapshot
PSICOV: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments
inferredcites →https://doi.org/10.1093/bioinformatics/btt259openalex-snapshot
PconsC: combination of direct information methods and alignments improves contact prediction
inferredcites →https://doi.org/10.1093/bioinformatics/btt260openalex-snapshot
InterEvScore: a novel coarse-grained interface scoring function using a multi-body statistical potential coupled to evolution
inferredcites →https://doi.org/10.1093/bioinformatics/btt440openalex-snapshot
High-accuracy prediction of transmembrane inter-helix contacts and application to GPCR 3D structure modeling
inferredcites →https://doi.org/10.1093/bioinformatics/btu500openalex-snapshot
CCMpred—fast and precise prediction of protein residue–residue contacts from correlated mutations
inferredcites →https://doi.org/10.1093/bioinformatics/btu791openalex-snapshot
MetaPSICOV: combining coevolution methods for accurate prediction of contacts and long range hydrogen bonding in proteins
inferredcites →https://doi.org/10.1093/bioinformatics/btv041openalex-snapshot
bbcontacts: prediction of β -strand pairing from direct coupling patterns
inferredcites →https://doi.org/10.1093/bioinformatics/btw618openalex-snapshot
Comparing co-evolution methods and their application to template-free protein structure prediction
inferredcites →https://doi.org/10.1093/bioinformatics/btz496openalex-snapshot
iScore: a novel graph kernel-based function for scoring protein–protein docking models
inferredcites →https://doi.org/10.1093/molbev/mss097openalex-snapshot
Sequence Evolution Correlates with Structural Dynamics
inferredcites →https://doi.org/10.1093/molbev/msv211openalex-snapshot
Coevolutionary Landscape Inference and the Context-Dependence of Mutations in Beta-Lactamase TEM-1
inferredcites →https://doi.org/10.1093/nar/gkt1223openalex-snapshot
Pfam: the protein families database
inferredcites →https://doi.org/10.1093/protein/14.11.835openalex-snapshot
Prediction of contact maps with neural networks and correlated mutations
inferredcites →https://doi.org/10.1093/protein/15.2.65openalex-snapshot
Use of covariance analysis for the prediction of structural domain boundaries from multiple protein sequence alignments
inferredcites →https://doi.org/10.1093/protein/7.3.349openalex-snapshot
Can three-dimensional contacts in protein structures be predicted by analysis of correlated mutations?
inferredcites →https://doi.org/10.1103/physreve.87.012707openalex-snapshot
Improved contact prediction in proteins: Using pseudolikelihoods to infer Potts models
inferredcites →https://doi.org/10.1107/s2052252516008113openalex-snapshot
Residue contacts predicted by evolutionary covariance extend the application of ab initio molecular replacement to larger and more challenging protein folds
inferredcites →https://doi.org/10.1107/s2052252517005115openalex-snapshot
Applications of contact predictions to structural biology
inferredcites →https://doi.org/10.1126/science.aah4043openalex-snapshot
Protein structure determination using metagenome sequence data
inferredcites →https://doi.org/10.1186/1471-2105-13-263openalex-snapshot
Improving the thermostability of alpha-amylase by combinatorial coevolving-site saturation mutagenesis
inferredcites →https://doi.org/10.1186/1471-2105-15-85openalex-snapshot
FreeContact: fast and free software for protein contact prediction from residue co-evolution
inferredcites →https://doi.org/10.1214/lnms/1215455556openalex-snapshot
Correlated mutations in models of protein sequences: phylogenetic and structural effects
inferredcites →https://doi.org/10.1371/journal.pcbi.1003776openalex-snapshot
The Fitness Landscape of HIV-1 Gag: Advanced Modeling Approaches and Validation of Model Predictions by In Vitro Testing
inferredcites →https://doi.org/10.1371/journal.pcbi.1003889openalex-snapshot
Improved Contact Predictions Using the Recognition of Protein Like Contact Patterns
inferredcites →https://doi.org/10.1371/journal.pcbi.1004262openalex-snapshot
Large-Scale Conformational Transitions and Dimerization Are Encoded in the Amino-Acid Sequences of Hsp70 Chaperones
inferredcites →https://doi.org/10.1371/journal.pcbi.1005324openalex-snapshot
Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model
inferredcites →https://doi.org/10.1371/journal.pone.0028766openalex-snapshot
Protein 3D Structure Computed from Evolutionary Sequence Variation
inferredcites →https://doi.org/10.1371/journal.pone.0108438openalex-snapshot
Combining Physicochemical and Evolutionary Information for Protein Contact Prediction
inferredcites →https://doi.org/10.1371/journal.pone.0143245openalex-snapshot
Coevolution Analysis of HIV-1 Envelope Glycoprotein Complex
inferredcites →https://doi.org/10.1371/journal.pone.0149166openalex-snapshot
Inter-Protein Sequence Co-Evolution Predicts Known Physical Interactions in Bacterial Ribosomes and the Trp Operon
inferredcites →https://doi.org/10.48550/arxiv.1510.04612openalex-snapshot
Quantification of the effect of mutations using a global probability model of natural sequence variation
inferredcites →https://doi.org/10.7554/elife.02030openalex-snapshot
Robust and accurate prediction of residue–residue interactions across protein interfaces using evolutionary information
inferredcites →https://doi.org/10.7554/elife.03430openalex-snapshot
Sequence co-evolution gives 3D contacts and structures of protein complexes
inferredcites →https://doi.org/10.7554/elife.09248openalex-snapshot
Large-scale determination of previously unsolved protein structures using evolutionary information

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1002/pro.3448openalex-snapshot
Integrating co‐evolutionary signals and other properties of residue pairs to distinguish biological interfaces from crystal contacts
inferred← citeshttps://doi.org/10.1007/s11517-024-03074-3openalex-snapshot
From PDB files to protein features: a comparative analysis of PDB bind and STCRDAB datasets
inferred← citeshttps://doi.org/10.1016/bs.apcsb.2024.11.007openalex-snapshot
Mapping the pathogenic nexus: Gene overlap and protein interaction networks in Alzheimer’s and breast cancer as a precursor to protein structure prediction and analysis
inferred← citeshttps://doi.org/10.1016/j.mcpro.2025.101065openalex-snapshot
State-of-the-Art and Future Directions in Structural Proteomics
inferred← citeshttps://doi.org/10.1038/s41598-019-55047-4openalex-snapshot
StructureDistiller: Structural relevance scoring identifies the most informative entries of a contact map
inferred← citeshttps://doi.org/10.1038/s41598-023-42090-5openalex-snapshot
Enhanced antibody-antigen structure prediction from molecular docking using AlphaFold2
inferred← citeshttps://doi.org/10.1093/bioinformatics/btab049openalex-snapshot
ConPlot: web-based application for the visualization of protein contact maps integrated with other data
inferred← citeshttps://doi.org/10.1093/bioinformatics/btx722openalex-snapshot
Sequential search leads to faster, more efficient fragment-basedde novoprotein structure prediction
inferred← citeshttps://doi.org/10.1093/bioinformatics/bty341openalex-snapshot
High precision in protein contact prediction using fully convolutional neural networks and minimal sequence features
inferred← citeshttps://doi.org/10.1093/bioinformatics/bty924openalex-snapshot
Improved inference of intermolecular contacts through protein–protein interaction prediction using coevolutionary analysis
inferred← citeshttps://doi.org/10.1093/bioinformatics/btz422openalex-snapshot
AlphaFold at CASP13
inferred← citeshttps://doi.org/10.1093/bioinformatics/btz496openalex-snapshot
iScore: a novel graph kernel-based function for scoring protein–protein docking models
inferred← citeshttps://doi.org/10.1101/2025.09.12.675843openalex-snapshot
PlasmoFP: leveraging deep learning to predict protein function of uncharacterized proteins across the malaria parasite genus
inferred← citeshttps://doi.org/10.1101/697839openalex-snapshot
StructureDistiller: Structural relevance scoring increases resilience of contact maps to false positive predictions
inferred← citeshttps://doi.org/10.1107/s2059798319013962openalex-snapshot
Molecular replacement using structure predictions from databases
inferred← citeshttps://doi.org/10.1111/mmi.15169openalex-snapshot
Co‐evolution at protein–protein interfaces guides inference of stoichiometry of oligomeric protein complexes by de novo structure prediction
inferred← citeshttps://doi.org/10.1186/s12859-019-2932-0openalex-snapshot
ProteinNet: a standardized data set for machine learning of protein structure
inferred← citeshttps://doi.org/10.12688/f1000research.14870.1openalex-snapshot
Combined approaches from physics, statistics, and computer science for ab initio protein structure prediction: ex unitate vires (unity is strength)?
inferred← citeshttps://doi.org/10.18174/547092openalex-snapshot
In silico protein science: from sequence to network
inferred← citeshttps://doi.org/10.19153/cleiej.24.2.3openalex-snapshot
Performance Analysis of Deep Learning Methods for Protein Contact Prediction in CASP13
inferred← citeshttps://doi.org/10.2174/0115680266259310230924190213openalex-snapshot
Computational Analysis of Gastric Canceromics Data to Identify Putative Biomarkers
inferred← citeshttps://doi.org/10.32607/20758251-2019-11-1-74-80openalex-snapshot
CASBench: A Benchmarking Set of Proteins with Annotated Catalytic and Allosteric Sites in Their Structures
inferred← citeshttps://doi.org/10.3390/biom10040626openalex-snapshot
Machine Learning Approaches for Quality Assessment of Protein Structures
inferred← citeshttps://doi.org/10.3390/genes15010025openalex-snapshot
When Protein Structure Embedding Meets Large Language Models
inferred← citeshttps://doi.org/10.3390/ijms232012688openalex-snapshot
Computational Docking Reveals Co-Evolution of C4 Carbon Delivery Enzymes in Diverse Plants
inferred← citeshttps://doi.org/10.70675/0dc56133z00acz4dffz8c7az0533f04cf409openalex-snapshot
Calcul efficace de la structure des protéines à partir de contacts évolutifs
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