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Direct-coupling analysis of residue coevolution captures native contacts across many protein families
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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Crystal Structures of the Response Regulator DosR from Mycobacterium tuberculosis Suggest a Helix Rearrangement Mechanism for Phosphorylation Activation
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Features of Protein–Protein Interactions in Two‐Component Signaling Deduced from Genomic Libraries
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Inference of Direct Residue Contacts in Two-Component Signaling
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Computational Modeling of Phosphotransfer Complexes in Two-Component Signaling
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Crystal Structure of Escherichia coli σE with the Cytoplasmic Domain of Its Anti-σ RseA
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Biological Sequence Analysis
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Separation of phylogenetic and functional associations in biological sequences by using the parametric bootstrap
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Identification of direct residue contacts in protein–protein interaction by message passing
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Respective roles of short- and long-range interactions in protein folding.
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How frequent are correlated changes in families of protein sequences?
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Crystal Structure of the Membrane Fusion Protein, MexA, of the Multidrug Transporter in Pseudomonas aeruginosa
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Solution of 'Solvable model of a spin glass'
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Convergence condition of the TAP equation for the infinite-ranged Ising spin glass model
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Profile hidden Markov models.
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Using multiple interdependency to separate functional from phylogenetic correlations in protein alignments
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Mutual information without the influence of phylogeny or entropy dramatically improves residue contact prediction
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The Pfam Protein Families Database
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The Pfam protein families database
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The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata
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Correlations Among Amino Acid Sites in bHLH Protein Domains: An Information Theoretic Analysis
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Can three-dimensional contacts in protein structures be predicted by analysis of correlated mutations?
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Regulation of the transcriptional activator NtrC1: structural studies of the regulatory and AAA + ATPase domains
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Information Theory and Statistical Mechanics
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Solvable Model of a Spin-Glass
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Determination of network of residues that regulate allostery in protein families using sequence analysis
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Comparison of anionic and cationic trypsinogens: The anionic activation domain is more flexible in solution and differs in its mode of BPTI binding in the crystal structure
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Evolutionarily Conserved Pathways of Energetic Connectivity in Protein Families
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Finding coevolving amino acid residues using row and column weighting of mutual information and multi-dimensional amino acid representation
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Disentangling Direct from Indirect Co-Evolution of Residues in Protein Alignments
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Dissecting the Specificity of Protein-Protein Interaction in Bacterial Two-Component Signaling: Orphans and Crosstalks
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3D Protein Structure Predicted from Sequence
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Incoming claims: where this work appears in other papers’ reference lists and arguments.
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A Global Eigenvalue-Driven Balanced Deconvolution Approach for Network Direct-Coupling Analysis
inferred← citeshttps://doi.org/10.1007/978-94-024-1069-3_2openalex-snapshot
Protein Structures, Interactions and Function from Evolutionary Couplings
inferred← citeshttps://doi.org/10.1007/978-94-024-1069-3_4openalex-snapshot
Comparative Protein Structure Modelling
inferred← citeshttps://doi.org/10.1007/978-981-13-2200-6_10openalex-snapshot
A Hybrid Approach for Protein Structure Determination Combining Sparse NMR with Evolutionary Coupling Sequence Data
inferred← citeshttps://doi.org/10.1007/978-981-13-2200-6_9openalex-snapshot
Prediction of Structures and Interactions from Genome Information
inferred← citeshttps://doi.org/10.1007/978-981-13-8719-7_15openalex-snapshot
Engineering Allostery into Proteins
inferred← citeshttps://doi.org/10.1007/978-981-13-8719-7_9openalex-snapshot
Interrogating Regulatory Mechanisms in Signaling Proteins by Allosteric Inhibitors and Activators: A Dynamic View Through the Lens of Residue Interaction Networks
inferred← citeshttps://doi.org/10.1007/978-981-96-9582-9_7openalex-snapshot
Protein-Protein Contact Prediction Using Structure-Informed Sequences and Protein Language Models
inferred← citeshttps://doi.org/10.1007/978-981-97-0060-8_7openalex-snapshot
System Biology and Protein Structure Prediction by Computer
inferred← citeshttps://doi.org/10.1007/s00018-013-1458-2openalex-snapshot
The functional importance of co-evolving residues in proteins
inferred← citeshttps://doi.org/10.1007/s00239-026-10329-0openalex-snapshot
Classification of SARS-CoV-2 Variants Through the Epistatic Circos Plots with Convolutional Neural Networks
inferred← citeshttps://doi.org/10.1007/s00239-026-10348-xopenalex-snapshot
Selection for Folding Stability Predicts Observed Covariation Between Protein Positions in the PDB
inferred← citeshttps://doi.org/10.1007/s00239-026-10353-0openalex-snapshot
Hierarchical Organization of Evolutionary Constraint in Duplicated EF-Hand Motifs
inferred← citeshttps://doi.org/10.1007/s00249-020-01480-7openalex-snapshot
Inferring functional units in ion channel pores via relative entropy
inferred← citeshttps://doi.org/10.1007/s00249-021-01500-0openalex-snapshot
Evolution of frustrated and stabilising contacts in reconstructed ancient proteins
inferred← citeshttps://doi.org/10.1007/s00439-022-02457-6openalex-snapshot
Genome interpretation using in silico predictors of variant impact
inferred← citeshttps://doi.org/10.1007/s00894-014-2497-9openalex-snapshot
Characteristics of protein residue-residue contacts and their application in contact prediction
inferred← citeshttps://doi.org/10.1007/s10462-022-10350-xopenalex-snapshot
Artificial intelligence for template-free protein structure prediction: a comprehensive review
inferred← citeshttps://doi.org/10.1007/s10601-020-09315-0openalex-snapshot
The potential of quantum annealing for rapid solution structure identification
inferred← citeshttps://doi.org/10.1007/s10955-015-1441-4openalex-snapshot
On the Entropy of Protein Families
inferred← citeshttps://doi.org/10.1007/s12038-022-00290-7openalex-snapshot
Nucleotide-based genetic networks: Methods and applications
inferred← citeshttps://doi.org/10.1007/s12250-013-3348-zopenalex-snapshot
Inference of global HIV-1 sequence patterns and preliminary feature analysis
inferred← citeshttps://doi.org/10.1007/s12551-022-01005-wopenalex-snapshot
Intragenic compensation through the lens of deep mutational scanning
inferred← citeshttps://doi.org/10.1007/s40042-022-00420-2openalex-snapshot
Temperature-dependent performance of the erasure machine
inferred← citeshttps://doi.org/10.1007/s40484-015-0045-yopenalex-snapshot
Determination of specificity influencing residues for key transcription factor families
inferred← citeshttps://doi.org/10.1016/0009-2614(90)85614-iopenalex-snapshot
Phase shifts induced by transient Bloch-Siegert effects in NMR
inferred← citeshttps://doi.org/10.1016/b978-0-12-374984-0.00613-6openalex-snapshot
Genetic Covariance
inferred← citeshttps://doi.org/10.1016/b978-0-12-394292-0.00002-3openalex-snapshot
Mining Tertiary Structural Motifs for Assessment of Designability
inferred← citeshttps://doi.org/10.1016/b978-0-12-394292-0.00009-6openalex-snapshot
Using Analyses of Amino Acid Coevolution to Understand Protein Structure and Function
inferred← citeshttps://doi.org/10.1016/b978-0-12-809633-8.12366-0openalex-snapshot
Computational Tools for Structural Analysis of Proteins
inferred← citeshttps://doi.org/10.1016/b978-0-12-809633-8.20147-7openalex-snapshot
Assessment of Structure Quality (RNA and Protein)
inferred← citeshttps://doi.org/10.1016/b978-0-12-809633-8.20505-0openalex-snapshot
Protein Three-Dimensional Structure Prediction
inferred← citeshttps://doi.org/10.1016/b978-0-12-816034-3.00007-9openalex-snapshot
Artificial intelligence in bioinformatics
inferred← citeshttps://doi.org/10.1016/b978-0-323-85707-9.00015-0openalex-snapshot
An Evolutionary Affair – The connection between Gaucher disease and Parkinson's disease
inferred← citeshttps://doi.org/10.1016/b978-0-323-95502-7.00261-xopenalex-snapshot
Computational Protein Engineering
inferred← citeshttps://doi.org/10.1016/b978-0-323-95502-7.00304-3openalex-snapshot
Assessment of Structure Quality (RNA and Protein)
inferred← citeshttps://doi.org/10.1016/b978-0-323-99507-8.00025-1openalex-snapshot
Energy landscapes in protein folding
inferred← citeshttps://doi.org/10.1016/b978-0-323-99507-8.00090-1openalex-snapshot
Biophysics of protein design
inferred← citeshttps://doi.org/10.1016/b978-0-323-99893-2.00002-6openalex-snapshot
AlphaFold, the successful prediction of three-dimensional protein structures and its impact on structural biology
inferred← citeshttps://doi.org/10.1016/b978-0-44-332908-1.00022-2openalex-snapshot
Deep learning for protein secondary structure prediction
inferred← citeshttps://doi.org/10.1016/b978-0-44-332908-1.00023-4openalex-snapshot
Deep learning in protein structure prediction
inferred← citeshttps://doi.org/10.1016/b978-0-443-31550-3.00014-7openalex-snapshot
Molecular structure and role of microbial proteins: a delimitation employing bioinformatics techniques
inferred← citeshttps://doi.org/10.1016/bs.apcsb.2015.07.003openalex-snapshot
RETRACTED: Theory, Methods, and Applications of Coevolution in Protein Contact Prediction
inferred← citeshttps://doi.org/10.1016/bs.apcsb.2019.12.005openalex-snapshot
Role of protein-protein interactions in allosteric drug design for DNA methyltransferases
inferred← citeshttps://doi.org/10.1016/bs.apcsb.2021.12.001openalex-snapshot
Computational prediction of protein functional sites—Applications in biotechnology and biomedicine
inferred← citeshttps://doi.org/10.1016/bs.mie.2018.11.004openalex-snapshot
Combining Evolutionary Covariance and NMR Data for Protein Structure Determination
inferred← citeshttps://doi.org/10.1016/bs.mie.2020.06.001openalex-snapshot
The use of consensus sequence information to engineer stability and activity in proteins
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Combining small angle X-ray scattering (SAXS) with protein structure predictions to characterize conformations in solution
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Improved protein relative solvent accessibility prediction using deep multi-view feature learning framework
inferred← citeshttps://doi.org/10.1016/j.abb.2014.05.010openalex-snapshot
Evolution of protein interactions: From interactomes to interfaces
inferred← citeshttps://doi.org/10.1016/j.abb.2019.108161openalex-snapshot
Integrating disorder in globular multidomain proteins: Fuzzy sensors and the role of SH3 domains
inferred← citeshttps://doi.org/10.1016/j.ajhg.2021.06.011openalex-snapshot
New approaches to predict the effect of co-occurring variants on protein characteristics
inferred← citeshttps://doi.org/10.1016/j.asoc.2015.06.024openalex-snapshot
Soft computing methods for the prediction of protein tertiary structures: A survey
inferred← citeshttps://doi.org/10.1016/j.bbagen.2019.07.008openalex-snapshot
Data-driven computational analysis of allosteric proteins by exploring protein dynamics, residue coevolution and residue interaction networks
inferred← citeshttps://doi.org/10.1016/j.bbamcr.2014.10.014openalex-snapshot
Structure–function analysis of NEET proteins uncovers their role as key regulators of iron and ROS homeostasis in health and disease
inferred← citeshttps://doi.org/10.1016/j.bbamem.2017.10.004openalex-snapshot
Applications of sequence coevolution in membrane protein biochemistry
inferred← citeshttps://doi.org/10.1016/j.bbapap.2026.141170openalex-snapshot
Local energetic frustration: Protein evolution, conformational dynamics and design in the age of AI
inferred← citeshttps://doi.org/10.1016/j.bbrc.2016.01.188openalex-snapshot
Improving residue–residue contact prediction via low-rank and sparse decomposition of residue correlation matrix
inferred← citeshttps://doi.org/10.1016/j.bbrc.2017.01.041openalex-snapshot
Sequence, structure and function relationships in flaviviruses as assessed by evolutive aspects of its conserved non-structural protein domains
inferred← citeshttps://doi.org/10.1016/j.bbrc.2026.154177openalex-snapshot
Residue interaction chains facilitating the structural change of ND6 subunit in respiratory complex I
inferred← citeshttps://doi.org/10.1016/j.bej.2021.107926openalex-snapshot
Improving thermostability of (R)-selective amine transaminase from Aspergillus terreus by evolutionary coupling saturation mutagenesis
inferred← citeshttps://doi.org/10.1016/j.bej.2024.109510openalex-snapshot
Cutting-edge computational approaches in enzyme design and activity enhancement
inferred← citeshttps://doi.org/10.1016/j.biochi.2014.12.007openalex-snapshot
Evolution, energy landscapes and the paradoxes of protein folding
inferred← citeshttps://doi.org/10.1016/j.biotechadv.2022.107926openalex-snapshot
Hot spots-making directed evolution easier
inferred← citeshttps://doi.org/10.1016/j.biotechadv.2023.108094openalex-snapshot
Role of distal sites in enzyme engineering
inferred← citeshttps://doi.org/10.1016/j.biotechadv.2025.108660openalex-snapshot
Capturing intrinsic protein dynamics for explaining beneficial substitutions from protein engineering campaigns
inferred← citeshttps://doi.org/10.1016/j.biotechadv.2025.108788openalex-snapshot
From traditional to AI-driven: The evolution of intelligent enzyme engineering for biocatalysis
inferred← citeshttps://doi.org/10.1016/j.bpc.2021.106552openalex-snapshot
Effects of pH on an IDP conformational ensemble explored by molecular dynamics simulation
inferred← citeshttps://doi.org/10.1016/j.bpj.2015.06.004openalex-snapshot
Structure-Encoded Global Motions and Their Role in Mediating Protein-Substrate Interactions
inferred← citeshttps://doi.org/10.1016/j.bpj.2016.04.039openalex-snapshot
Structure of the Bacterial Cytoskeleton Protein Bactofilin by NMR Chemical Shifts and Sequence Variation
inferred← citeshttps://doi.org/10.1016/j.bpj.2017.02.029openalex-snapshot
The Role of Evolutionary Selection in the Dynamics of Protein Structure Evolution
inferred← citeshttps://doi.org/10.1016/j.bpj.2017.08.039openalex-snapshot
How Many Protein Sequences Fold to a Given Structure? A Coevolutionary Analysis
inferred← citeshttps://doi.org/10.1016/j.bpj.2017.10.028openalex-snapshot
Coevolutionary Landscape of Kinase Family Proteins: Sequence Probabilities and Functional Motifs
inferred← citeshttps://doi.org/10.1016/j.bpj.2019.04.006openalex-snapshot
Learning the Formation Mechanism of Domain-Level Chromatin States with Epigenomics Data
inferred← citeshttps://doi.org/10.1016/j.bpj.2019.05.008openalex-snapshot
Conformational Dynamics and Cooperativity Drive the Specificity of a Protein-Ligand Interaction
inferred← citeshttps://doi.org/10.1016/j.bpj.2019.09.001openalex-snapshot
Evolutionarily Conserved Interactions within the Pore Domain of Acid-Sensing Ion Channels
inferred← citeshttps://doi.org/10.1016/j.bpj.2019.09.040openalex-snapshot
Coevolutionary Couplings Unravel PAM-Proximal Constraints of CRISPR-SpCas9
inferred← citeshttps://doi.org/10.1016/j.bpj.2020.12.018openalex-snapshot
Frustration and Direct-Coupling Analyses to Predict Formation and Function of Adeno-Associated Virus
inferred← citeshttps://doi.org/10.1016/j.bpj.2021.03.036openalex-snapshot
Electrostatic interaction optimization improves catalytic rates and thermotolerance on xylanases
inferred← citeshttps://doi.org/10.1016/j.bpj.2021.09.032openalex-snapshot
Switching an active site helix in dihydrofolate reductase reveals limits to subdomain modularity
inferred← citeshttps://doi.org/10.1016/j.bpj.2022.05.036openalex-snapshot
Computational compensatory mutation discovery approach: Predicting a PARP1 variant rescue mutation
inferred← citeshttps://doi.org/10.1016/j.bpj.2023.06.009openalex-snapshot
Characterizing interactions in E-cadherin assemblages
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