ArticleThe journal of physical chemistry. B2013
Population based reweighting of scaled molecular dynamics.
Article in The journal of physical chemistry. B, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
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Who cites it
43 citing papers in PubMed.
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- Conformational signatures induced by ubiquitin modification in the amyloid-forming tau repeat domain.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- ModBind, a Rapid Simulation-Based Predictor of Ligand Binding and Off-Rates.Journal of chemical information and modeling · 2025Article
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- Flexible Gaussian Accelerated Molecular Dynamics to Enhance Biological Sampling.Journal of chemical theory and computation · 2023Article
- Past, Present, and Future Perspectives on Computer-Aided Drug Design Methodologies.Molecules (Basel, Switzerland) · 2023Review
- Predicting Biomolecular Binding Kinetics: A Review.Journal of chemical theory and computation · 2023Review
- Challenges and frontiers of computational modelling of biomolecular recognition.QRB discovery · 2022Article
- Enhanced-Sampling Simulations for the Estimation of Ligand Binding Kinetics: Current Status and Perspective.Frontiers in molecular biosciences · 2022Review
- Peptide stapling by late-stage Suzuki-Miyaura cross-coupling.Beilstein journal of organic chemistry · 2022Article
- Advanced Sampling Methods for Multiscale Simulation of Disordered Proteins and Dynamic Interactions.Biomolecules · 2021Review
- Reduced efficacy of a Src kinase inhibitor in crowded protein solution.Nature communications · 2021Article
- DESP: Deep Enhanced Sampling of Proteins' Conformation Spaces Using AI-Inspired Biasing Forces.Frontiers in molecular biosciences · 2021Article
- Thermodynamics and Kinetics of Drug-Target Binding by Molecular Simulation.Chemical reviews · 2020Review
- Dynamic design: manipulation of millisecond timescale motions on the energy landscape of cyclophilin A.Chemical science · 2020Article
- pH-Induced Local Unfolding of the Phl p 6 Pollen Allergen From cpH-MD.Frontiers in molecular biosciences · 2020Article
- Exploring the PXR ligand binding mechanism with advanced Molecular Dynamics methods.Scientific reports · 2018Article
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4 authors.
Funding
Abstract
Molecular dynamics simulation using enhanced sampling methods is one of the powerful computational tools used to explore protein conformations and free energy landscapes. Enhanced sampling methods often employ either an increase in temperature or a flattening of the potential energy surface to rapidly sample phase space, and a corresponding reweighting algorithm is used to recover the Boltzmann statistics. However, potential energies of complex biomolecules usually involve large fluctuations on a magnitude of hundreds of kcal/mol despite minimal structural changes during simulation. This leads to noisy reweighting statistics and complicates the obtainment of accurate final results. To overcome this common issue in enhanced conformational sampling, we propose a scaled molecular dynamics method, which modifies the biomolecular potential energy surface and employs a reweighting scheme based on configurational populations. Statistical mechanical theory is applied to derive the reweighting formula, and the canonical ensemble of simulated structures is recovered accordingly. Test simulations on alanine dipeptide and the fast folding polypeptide Chignolin exhibit sufficiently enhanced conformational sampling and accurate recovery of free energy surfaces and thermodynamic properties. The results are comparable to long conventional molecular dynamics simulations and exhibit better recovery of canonical statistics over methods which employ a potential energy term in reweighting.
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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.