ArticleThe journal of physical chemistry. A2021
A Minimal, Adaptive Binning Scheme for Weighted Ensemble Simulations.
Article in The journal of physical chemistry. A, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed.
- A Minimalist Model for Navigating Conformational Landscape Uncovers the Activation Mechanism of βACS physical chemistry Au · 2026Article
- Pathway representationDigital discovery · 2026Article
- Large-scale protein conformational transitions revealed by weighted ensemble simulations and EPR.Chemical science · 2026Article
- Pathway Representation via Intrinsic Structural Medoids (PRISM): A Structural Mapping Approach to Clustering Molecular Pathways.bioRxiv : the preprint server for biology · 2026Article
- D614G reshapes allosteric networks and opening mechanisms of SARS-CoV-2 spikes.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Generation of Pathway Signatures by Combining Normal Modes with Weighted Ensemble Simulations.bioRxiv : the preprint server for biology · 2026Article
- Rectifying AI-generated protein structure ensembles for equilibrium using physics-based computations.bioRxiv : the preprint server for biology · 2026Article
- Reducing weighted ensemble variance with optimal trajectory management.The Journal of chemical physics · 2026Article
- Weighted Ensemble Simulations Reveal Novel Conformations and Modulator Effects in Hepatitis B Virus Capsid Assembly.Journal of chemical theory and computation · 2025Article
- Weighted Ensemble Simulations With the Drude Polarizable Model.Journal of computational chemistry · 2025Article
- Regulatory Interactions between APOBEC3B N- and C-Terminal Domains.Journal of chemical information and modeling · 2025Article
- Unsupervised Learning of Progress Coordinates during Weighted Ensemble Simulations: Application to NTL9 Protein Folding.Journal of chemical theory and computation · 2025Article
- Regulatory interactions between APOBEC3B N- and C-terminal domains.bioRxiv : the preprint server for biology · 2024Article
- Augmenting Human Expertise in Weighted Ensemble Simulations through Deep Learning-Based Information Bottleneck.Journal of chemical theory and computation · 2024Article
- Article
- Exploration of Cryptic Pockets Using Enhanced Sampling Along Normal Modes: A Case Study of KRASJournal of chemical information and modeling · 2024Article
- Gating residues govern ligand unbinding kinetics from the buried cavity in HIF-2α PAS-B.Protein science : a publication of the Protein Society · 2024Article
- System size effects on the free energy landscapes from molecular dynamics of phase-separating bilayers.The Journal of chemical physics · 2024Article
- Simulation-driven design of stabilized SARS-CoV-2 spike S2 immunogens.Nature communications · 2024Article
- Understanding the free-energy landscape of phase separation in lipid bilayers using molecular dynamics.Biophysical journal · 2023Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
A promising approach for simulating rare events with rigorous kinetics is the weighted ensemble path sampling strategy. One challenge of this strategy is the division of configurational space into bins for sampling. Here we present a minimal adaptive binning (MAB) scheme for the automated, adaptive placement of bins along a progress coordinate within the framework of the weighted ensemble strategy. Results reveal that the MAB binning scheme, despite its simplicity, is more efficient than a manual, fixed binning scheme in generating transitions over large free energy barriers, generating a diversity of pathways, estimating rate constants, and sampling conformations. The scheme is general and extensible to any rare-events sampling strategy that employs progress coordinates.
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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.