ArticleMolecular biology and evolution2016
Coevolutionary Landscape Inference and the Context-Dependence of Mutations in Beta-Lactamase TEM-1.
Article in Molecular biology and evolution, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 151 papers.
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Who cites it
151 citing papers in PubMed, 305 citations in OpenAlex.
- Protein stability is determined by single-site bias rather than pairwise covariance.Nature chemical biology · 2026Article
- Scanning the horizon: deep mutational scanning approaches in virology.Journal of virology · 2026Review
- Proteome-wide prediction of the functional impact of missense variants with ProteoCast.Nature communications · 2026Article
- Origins and breadth of pairwise epistasis in an α-helix of β-lactamase TEM-1.Nature communications · 2026Article
- Functional bottlenecks can emerge from non-epistatic underlying traits.PLoS computational biology · 2026Article
- MODEL-FREE INFERENCE FOR CHARACTERIZING PROTEIN MUTATIONS THROUGH A COEVOLUTIONARY LENS.The annals of applied statistics · 2026Article
- Controllable protein design via autoregressive direct coupling analysis conditioned on principal components.PLoS computational biology · 2026Article
- Probing the dark energy in the functional protein universe.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Predicting Protein Folding Dynamics Using Sequence Information.Methods in molecular biology (Clifton, N.J.) · 2026Article
- adabmDCA 2.0-A Flexible but Easy-to-Use Package for Direct Coupling Analysis.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Deep mutational scans clarify the record of evolution.Nature ecology & evolution · 2025Article
- Epistatic drift in protein evolution.Current opinion in genetics & development · 2025Review
- Inferring protein-folding mechanisms from natural sequence diversity.Biophysical journal · 2025Article
- Exploring sequence- and structure-based fitness landscapes to enhance thermal resistance and activity of endoglucanase II with minimal experimental effort.RSC chemical biology · 2025Article
- Thermal Adaptation of Cytosolic Malate Dehydrogenase Revealed by Deep Learning and Coevolutionary Analysis.Journal of chemical theory and computation · 2025Article
- Exploring Evolution to Uncover Insights Into Protein Mutational Stability.Molecular biology and evolution · 2025Article
- MMRT: MultiMut Recursive Tree for predicting functional effects of high-order protein variants from low-order variants.Computational and structural biotechnology journal · 2025Article
- Generating Artificial Ribozymes Using Sparse Coevolutionary Models.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Combining evolution and protein language models for an interpretable cancer driver mutation prediction with D2Deep.Briefings in bioinformatics · 2024Article
- Emergent time scales of epistasis in protein evolution.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
91 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors at 3 institutions in 2 countries.
Funding
Abstract
The quantitative characterization of mutational landscapes is a task of outstanding importance in evolutionary and medical biology: It is, for example, of central importance for our understanding of the phenotypic effect of mutations related to disease and antibiotic drug resistance. Here we develop a novel inference scheme for mutational landscapes, which is based on the statistical analysis of large alignments of homologs of the protein of interest. Our method is able to capture epistatic couplings between residues, and therefore to assess the dependence of mutational effects on the sequence context where they appear. Compared with recent large-scale mutagenesis data of the beta-lactamase TEM-1, a protein providing resistance against beta-lactam antibiotics, our method leads to an increase of about 40% in explicative power as compared with approaches neglecting epistasis. We find that the informative sequence context extends to residues at native distances of about 20 Å from the mutated site, reaching thus far beyond residues in direct physical contact.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.