ReviewAnnual review of biophysics2017
Weighted Ensemble Simulation: Review of Methodology, Applications, and Software.
Review in Annual review of biophysics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 163 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
163 citing papers in PubMed.
- A Minimalist Model for Navigating Conformational Landscape Uncovers the Activation Mechanism of βACS physical chemistry Au · 2026Article
- Assessing the Stability of Molecular Glues with Weighted Ensemble Simulations.Journal of chemical theory and computation · 2026Article
- Comparing Enhanced Sampling Methods in Exploring the Conformational Space of β-CateninThe journal of physical chemistry. B · 2026Article
- AI-Physics-Experiment Trinity for Integrated Protein Dynamics Modeling.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- Polyproline Modulates Membrane Translocation of Arginine-Rich Cell-Penetrating Peptides: Insights from Molecular Dynamics Simulations.The Journal of membrane 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
- The Open Molecular Software Foundation (OMSF) and the Growing Role of Open Source Software in Molecular Modeling.Journal of chemical information and modeling · 2026Review
- Reducing weighted ensemble variance with optimal trajectory management.The Journal of chemical physics · 2026Article
- Advances in molecular dynamics approaches for investigating cell-penetrating peptides.Biophysical reviews · 2026Review
- Allosteric Activation through Coordinated Energy Landscape Reweighting and Information Flow.Computational and structural biotechnology journal · 2026Article
- Weighted Ensemble Simulations Reveal Novel Conformations and Modulator Effects in Hepatitis B Virus Capsid Assembly.Journal of chemical theory and computation · 2025Article
- Cryo-electron microscopy ensemble optimization using individual particles and physical constraints.bioRxiv : the preprint server for biology · 2025Article
- Weighted Ensemble Simulations With the Drude Polarizable Model.Journal of computational chemistry · 2025Article
- High-Throughput Computation of Anharmonic Low-Frequency Protein Vibrations.The journal of physical chemistry. B · 2025Article
- Unbiased Enhanced Sampling in Molecular Dynamics via Simultaneously Accelerating Diffusion in Multiple Low-Dimensional Collective Variable Spaces.Journal of chemical theory and computation · 2025Article
- Integrating Hydrogen Exchange with Molecular Dynamics for Improved Ligand Binding Predictions.Journal of chemical information and modeling · 2025Article
- High-Throughput Ligand Dissociation Kinetics Predictions Using Site Identification by Ligand Competitive Saturation.Journal of chemical theory and computation · 2025Article
- Hidden GPCR structural transitions addressed by multiple walker supervised molecular dynamics (mwSuMD).eLife · 2025Article
103 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
Abstract
The weighted ensemble (WE) methodology orchestrates quasi-independent parallel simulations run with intermittent communication that can enhance sampling of rare events such as protein conformational changes, folding, and binding. The WE strategy can achieve superlinear scaling-the unbiased estimation of key observables such as rate constants and equilibrium state populations to greater precision than would be possible with ordinary parallel simulation. WE software can be used to control any dynamics engine, such as standard molecular dynamics and cell-modeling packages. This article reviews the theoretical basis of WE and goes on to describe successful applications to a number of complex biological processes-protein conformational transitions, (un)binding, and assembly processes, as well as cell-scale processes in systems biology. We furthermore discuss the challenges that need to be overcome in the next phase of WE methodological development. Overall, the combined advances in WE methodology and software have enabled the simulation of long-timescale processes that would otherwise not be practical on typical computing resources using standard simulation.
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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.