ReviewPLoS computational biology2016
Revealing Atomic-Level Mechanisms of Protein Allostery with Molecular Dynamics Simulations.
Review in PLoS computational biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 51 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
51 citing papers in PubMed.
- The SlpX protein of Lactobacillus acidophilus CICC6074 has anti-inflammatory properties and protects Caco-2 intestinal epithelial cells from TNF-α-induced barrier damage.Journal of the science of food and agriculture · 2026Article
- Computational Identification of Potential Novel Allosteric IHF Inhibitors Using QSAR Modeling to Inhibit Plasmid-Mediated Antibiotic Resistance.International journal of molecular sciences · 2026Article
- Mapping Allosteric Communication in the Nucleosome with Conditional Activity.Journal of chemical information and modeling · 2026Article
- Mechanisms of Okanin against wound healing based on network pharmacology, molecular docking and molecular dynamics simulation.Scientific reports · 2025Article
- Artificial intelligence in protein-based detection and inhibition of AMR pathways.Journal of computer-aided molecular design · 2025Review
- Mapping Allosteric Communication in the Nucleosome with Conditional Activity.bioRxiv : the preprint server for biology · 2025Article
- Visualizing agonist-induced M2 receptor activation regulated by aromatic ring dynamics.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Exploring Binding Sites in Chagas Disease Protein TcP21 Using Integrated Mixed Solvent Molecular Dynamics Approaches.Journal of chemical information and modeling · 2025Article
- Astragaloside IV ameliorates atrazine-induced male reproductive toxicity: anFrontiers in toxicology · 2025Article
- Special Issue: "Molecular Dynamics Simulations and Structural Analysis of Protein Domains".International journal of molecular sciences · 2024Article
- G protein-coupled receptors (GPCRs): advances in structures, mechanisms, and drug discovery.Signal transduction and targeted therapy · 2024Review
- Perspectives on Computational Enzyme Modeling: From Mechanisms to Design and Drug Development.ACS omega · 2024Review
- Mechanism of drug resistance in HIV-1 protease subtype C in the presence of Atazanavir.Current research in structural biology · 2024Article
- Computational insights into the mechanisms underlying structural destabilization and recovery in trafficking-deficient hERG mutants.Frontiers in molecular biosciences · 2024Article
- Article
- Structural basis of dimerization of chemokine receptors CCR5 and CXCR4.Nature communications · 2023Article
- Allosteric regulation of kinase activity in living cells.bioRxiv : the preprint server for biology · 2023Article
- Allosteric Signaling in PDZ Energetic Networks: Embedding Error Analysis.The journal of physical chemistry. B · 2023Article
- Variable Regions of p53 Isoforms Allosterically Hard Code DNA Interaction.The journal of physical chemistry. B · 2022Article
- Emerging Methods and Applications to Decrypt Allostery in Proteins and Nucleic Acids.Journal of molecular biology · 2022Review
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Molecular dynamics (MD) simulations have become a powerful and popular method for the study of protein allostery, the widespread phenomenon in which a stimulus at one site on a protein influences the properties of another site on the protein. By capturing the motions of a protein's constituent atoms, simulations can enable the discovery of allosteric binding sites and the determination of the mechanistic basis for allostery. These results can provide a foundation for applications including rational drug design and protein engineering. Here, we provide an introduction to the investigation of protein allostery using molecular dynamics simulation. We emphasize the importance of designing simulations that include appropriate perturbations to the molecular system, such as the addition or removal of ligands or the application of mechanical force. We also demonstrate how the bidirectional nature of allostery-the fact that the two sites involved influence one another in a symmetrical manner-can facilitate such investigations. Through a series of case studies, we illustrate how these concepts have been used to reveal the structural basis for allostery in several proteins and protein complexes of biological and pharmaceutical interest.
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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.