ReviewThe European physical journal. B2021
Dynamical nonequilibrium molecular dynamics reveals the structural basis for allostery and signal propagation in biomolecular systems.
Review in The European physical journal. B, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
What it found
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Who cites it
17 citing papers in PubMed, 48 citations in OpenAlex.
- Non-Equilibrium Molecular Dynamics Simulation Captures Potential New Drug Target: Ec-MscL Gating Mechanism Explored with External Electric Field.Antibiotics (Basel, Switzerland) · 2026Article
- Dynamical Nonequilibrium Molecular Dynamics Simulations Reveal Atomistic Steps of C-Type Inactivation in Cardiac hERG Channels.Journal of the American Chemical Society · 2026Article
- Dynamical-nonequilibrium alanine scanning for identifying allosteric positions in proteins.Biophysical journal · 2026Article
- Ligand-driven modulation of chaperone-cochaperone networks shapes proteostasis outcomes.Protein science : a publication of the Protein Society · 2026Article
- Second-order allosteric control as a mechanism for compensatory mutations in B-cell translocation gene 2.Protein science : a publication of the Protein Society · 2025Article
- Article
- Signal Propagation in the ATPase Domain ofBiochemistry · 2024Article
- Decrypting Allostery in Membrane-Bound K-Ras4B Using ComplementaryJournal of the American Chemical Society · 2024Article
- Fluctuation Relations to Calculate Protein Redox Potentials from Molecular Dynamics Simulations.Journal of chemical theory and computation · 2024Article
- SARS-CoV-2 spike variants differ in their allosteric responses to linoleic acid.Journal of molecular cell biology · 2023Article
- Article
- Exploring and Learning the Universe of Protein Allostery Using Artificial Intelligence Augmented Biophysical and Computational Approaches.Journal of chemical information and modeling · 2023Review
- #COVIDisAirborne: AI-enabled multiscale computational microscopy of delta SARS-CoV-2 in a respiratory aerosol.The international journal of high performance computing applications · 2023Article
- Structural insights in cell-type specific evolution of intra-host diversity by SARS-CoV-2.Nature communications · 2022Article
- The fatty acid site is coupled to functional motifs in the SARS-CoV-2 spike protein and modulates spike allosteric behaviour.Computational and structural biotechnology journal · 2022Article
- #COVIDisAirborne: AI-Enabled Multiscale Computational Microscopy of Delta SARS-CoV-2 in a Respiratory Aerosol.bioRxiv : the preprint server for biology · 2021Article
- Weighted Ensemble Simulation: Advances in methods, software, and applications.Wiley interdisciplinary reviews. Computational molecular scienceArticle
Corrections and comments
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Authors and funding
4 authors at 3 institutions in 3 countries.
Funding
Abstract
abstractA dynamical approach to nonequilibrium molecular dynamics (D-NEMD), proposed in the 1970s by Ciccotti et al., is undergoing a renaissance and is having increasing impact in the study of biological macromolecules. This D-NEMD approach, combining MD simulations in stationary (in particular, equilibrium) and nonequilibrium conditions, allows for the determination of the time-dependent structural response of a system using the Kubo-Onsager relation. Besides providing a detailed picture of the system's dynamic structural response to an external perturbation, this approach also has the advantage that the statistical significance of the response can be assessed. The D-NEMD approach has been used recently to identify a general mechanism of inter-domain signal propagation in nicotinic acetylcholine receptors, and allosteric effects in GRAPHIC ABSTRACT:
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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.