Protein structure prediction from sequence variation

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Direct-coupling analysis of residue coevolution captures native contacts across many 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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Correlated mutations and residue contacts 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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Systematic Validation of Protein Force Fields against Experimental Data

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Three-Dimensional Structures of Membrane Proteins from Genomic Sequencing

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

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Super-resolution biomolecular crystallography with low-resolution data

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NMR Structure Determination for Larger Proteins Using Backbone-Only Data

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How frequent are correlated changes in families of protein sequences?

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

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Genomics-aided structure prediction

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Determination of solution structures of proteins up to 40 kDa using CS-Rosetta with sparse NMR data from deuterated samples

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

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

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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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Mössbauer Spectroscopy of Biological Systems

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Structural perspectives on secondary active transporters

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Compensating changes in protein multiple sequence alignments

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CASP9 results compared to those of previous casp experiments

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Coevolution of PDZ domain–ligand interactions analyzed by high-throughput phage display and deep sequencing

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Gene3D: a domain-based resource for comparative genomics, functional annotation and protein network analysis

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CASP9 assessment of free modeling target predictions

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Structure–function mapping of a heptameric module in the nuclear pore complex

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Evaluation of residue–residue contact predictions in CASP9

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Progress in predicting inter-residue contacts of proteins with neural networks and correlated mutations

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Sampling Bottlenecks in De novo Protein Structure Prediction

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Assessment of domain boundary predictions and the prediction of intramolecular contacts in CASP8

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Improving Protein Structure Prediction Using Multiple Sequence-Based Contact Predictions

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Metagenomics and the protein universe

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Using Sequence Alignments to Predict Protein Structure and Stability With High AccuracyPreprint

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Protein topology from predicted residue contacts

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Highly accurate protein structure prediction with AlphaFold

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Mutation effects predicted from sequence co-variation

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AlphaFold and Implications for Intrinsically Disordered Proteins

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Robust and accurate prediction of residue–residue interactions across protein interfaces using evolutionary information

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Modeling the language of life – Deep Learning Protein Sequences

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Protein structure determination using metagenome sequence data

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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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Benchmarking <scp>AlphaFold</scp> for protein complex modeling reveals accuracy determinants

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An evolution-based model for designing chorismate mutase enzymes

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Benchmarking AlphaFold for protein complex modeling reveals accuracy determinants

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Protein design and variant prediction using autoregressive generative models

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Protein interaction networks revealed by proteome coevolution

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The Causes and Consequences of Genetic Interactions (Epistasis)

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Controlling Allosteric Networks in Proteins

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AlphaFold 2: Why It Works and Its Implications for Understanding the Relationships of Protein Sequence, Structure, and Function

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Large-scale determination of previously unsolved protein structures using evolutionary information

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Assessment of contact predictions in CASP12: Co‐evolution and deep learning coming of age

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3D RNA and Functional Interactions from Evolutionary Couplings

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Protein language model embeddings for fast, accurate, alignment-free protein structure prediction

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Conditional Selection of Genomic Alterations Dictates Cancer Evolution and Oncogenic Dependencies

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Blind prediction of homo- and hetero-protein complexes: the CASP13-CAPRI experiment

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Deep learning in biomedical data science

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AlphaFold2 reveals commonalities and novelties in protein structure space for 21 model organisms

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Harnessing generative AI to decode enzyme catalysis and evolution for enhanced engineering

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AlphaFold Models of Small Proteins Rival the Accuracy of Solution NMR Structures

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Assessment of prediction methods for protein structures determined by <scp>NMR</scp> in <scp>CASP14</scp> : Impact of <scp>AlphaFold2</scp>

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An end-to-end framework for the prediction of protein structure and fitness from single sequence

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Next Generation Protein Structure Predictions and Genetic Variant Interpretation

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Accurate protein stability predictions from homology models

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