ArticleWiley interdisciplinary reviews. Computational molecular science
Weighted Ensemble Simulation: Advances in methods, software, and applications.
Article in Wiley interdisciplinary reviews. Computational molecular science. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 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
- Free-Energy Landscapes of HBV Hexamer Closure Reveal Key Structural Features of the Transition.Journal of chemical theory and computation · 2026Article
- Pathway Representation via Intrinsic Structural Medoids (PRISM): A Structural Mapping Approach to Clustering Molecular Pathways.bioRxiv : the preprint server for biology · 2026Article
- The fine effects of high magnetic fields on hyperfine shifts.Chemical science · 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
- Oligomerisation and stereoselective polymerisation of alkenes and alkynes using pyridyl-based Al(iii) catalysts.Chemical science · 2026Article
- The Open Molecular Software Foundation (OMSF) and the Growing Role of Open Source Software in Molecular Modeling.Journal of chemical information and modeling · 2026Review
- Unlocking the undruggable spliceosome: generative AI and structural dynamics in cancer therapy.Frontiers in cell and developmental biology · 2026Review
- Solvation strategies for free-energy calculations in a halogen-bonded complex: implicit, explicit, and machine learning approaches.Chemical science · 2025Article
- Weighted Ensemble Simulations Reveal Novel Conformations and Modulator Effects in Hepatitis B Virus Capsid Assembly.Journal of chemical theory and computation · 2025Article
- Sustainable electrochemical synthesis of aliphatic nitro-Beilstein journal of organic chemistry · 2025Article
Corrections and comments
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Authors and funding
2 authors.
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Abstract
For more than two decades, weighted ensemble (WE) path sampling strategies have enabled the simulation of pathways for rare events-or barrier-crossing processes-with significantly less computing cost than conventional simulations, all while preserving rigorous kinetics. This review highlights recent advances in WE methods and software, including tools for mechanistic analysis of path ensembles and efficient estimation of rates. We showcase successful weighted ensemble applications across a wide range of condensed-phase processes, such as hybrid quantum mechanics/molecular mechanics (QM/MM) simulations of microsecond-timescale chemical reactions, and atomistic simulations of slower processes on the millisecond to seconds timescale. These applications span drug membrane permeation, ligand unbinding, and the large-scale opening of the SARS-CoV-2 spike protein. We also discuss the current limitations and key challenges facing WE strategies, which have yet to reach their full potential.
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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 Socratic graph.