ReviewComputational and structural biotechnology journal2016
Biophysical and computational methods to analyze amino acid interaction networks in proteins.
Review in Computational and structural biotechnology journal, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed.
- Free energy perturbations in enzyme kinetic models reveal cryptic epistasis.PLoS computational biology · 2026Article
- Structural determinants of non-covalent PPARγ inverse agonism and their therapeutic implications.Nature communications · 2025Article
- The Evolving Landscape of Protein Allostery: From Computational and Experimental Perspectives.Journal of molecular biology · 2025Review
- From Diarylsulfides to Diarylamines: New Ebola Virus Entry Inhibitors with Improved Metabolic Stability.Journal of medicinal chemistry · 2025Article
- Article
- Modulation of Allostery with Multiple Mechanisms by Hotspot Mutations in TetR.Journal of the American Chemical Society · 2024Article
- Pervasive epistasis exposes intramolecular networks in adaptive enzyme evolution.Nature communications · 2023Article
- Modulation of Allostery with Multiple Mechanisms by Hotspot Mutations in TetR.bioRxiv : the preprint server for biology · 2023Article
- Fishing for Catalysis: Experimental Approaches to Narrowing Search Space in Directed Evolution of Enzymes.JACS Au · 2023Review
- Visualizing the Residue Interaction Landscape of Proteins by Temporal Network Embedding.Journal of chemical theory and computation · 2023Article
- Neural relational inference to learn long-range allosteric interactions in proteins from molecular dynamics simulations.Nature communications · 2022Article
- SenseNet, a tool for analysis of protein structure networks obtained from molecular dynamics simulations.PloS one · 2022Article
- Compensatory epistasis explored by molecular dynamics simulations.Human genetics · 2021Article
- Structural basis of the selective activation of enzyme isoforms: Allosteric response to activators of β1- and β2-containing AMPK complexes.Computational and structural biotechnology journal · 2021Article
- Investigating Conformational Dynamics and Allostery in the p53 DNA-Binding Domain Using Molecular Simulations.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Computational study on the allosteric mechanism ofComputational and structural biotechnology journal · 2021Article
- Substitution of a Surface-Exposed Residue Involved in an Allosteric Network Enhances Tryptophan Synthase Function in Cells.Frontiers in molecular biosciences · 2021Article
- Protein conformational switch discerned via network centrality properties.Computational and structural biotechnology journal · 2021Article
- Elucidating the Activation Mechanism of AMPK by Direct Pan-Activator PF-739.Frontiers in molecular biosciences · 2021Article
- Multi-state design of flexible proteins predicts sequences optimal for conformational change.PLoS computational biology · 2020Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Globular proteins are held together by interacting networks of amino acid residues. A number of different structural and computational methods have been developed to interrogate these amino acid networks. In this review, we describe some of these methods, including analyses of X-ray crystallographic data and structures, computer simulations, NMR data, and covariation among protein sequences, and indicate the critical insights that such methods provide into protein function. This information can be leveraged towards the design of new allosteric drugs, and the engineering of new protein function and protein regulation strategies.
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