ArticleThe journal of physical chemistry. B2014
WExplore: hierarchical exploration of high-dimensional spaces using the weighted ensemble algorithm.
Article in The journal of physical chemistry. B, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 55 papers.
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Who cites it
55 citing papers in PubMed.
- Rectifying AI-generated protein structure ensembles for equilibrium using physics-based computations.bioRxiv : the preprint server for biology · 2026Article
- Hidden GPCR structural transitions addressed by multiple walker supervised molecular dynamics (mwSuMD).eLife · 2025Article
- Markov State Models with Weighted Ensemble Simulation: How to Eliminate the Trajectory Merging Bias.Journal of chemical theory and computation · 2025Article
- Augmenting Human Expertise in Weighted Ensemble Simulations through Deep Learning-Based Information Bottleneck.Journal of chemical theory and computation · 2024Article
- Article
- BAD-NEUS: Rapidly converging trajectory stratification.The Journal of chemical physics · 2024Article
- Quantitative Prediction of Dissociation Rates of PYK2 Ligands Using Umbrella Sampling and Milestoning.Journal of chemical theory and computation · 2024Article
- Exploring Kinase Asp-Phe-Gly (DFG) Loop Conformational Stability with AlphaFold2-RAVE.Journal of chemical information and modeling · 2024Article
- Biomolecular dynamics in the 21st century.Biochimica et biophysica acta. General subjects · 2024Review
- How Robust Is the Ligand Binding Transition State?Journal of the American Chemical Society · 2023Article
- Perspectives on Ligand/Protein Binding Kinetics Simulations: Force Fields, Machine Learning, Sampling, and User-Friendliness.Journal of chemical theory and computation · 2023Review
- Worth the Weight: Sub-Pocket EXplorer (SubPEx), a Weighted Ensemble Method to Enhance Binding-Pocket Conformational Sampling.Journal of chemical theory and computation · 2023Article
- Article
- Uncertainties in Markov State Models of Small Proteins.Journal of chemical theory and computation · 2023Article
- Flexible Topology: A Dynamic Model of a Continuous Chemical Space.Journal of chemical theory and computation · 2023Article
- pyCHARMM: Embedding CHARMM Functionality in a Python Framework.Journal of chemical theory and computation · 2023Article
- Worth the weight: Sub-Pocket EXplorer (SubPEx), a weighted-ensemble method to enhance binding-pocket conformational sampling.bioRxiv : the preprint server for biology · 2023Article
- Quality over quantity: Sampling high probability rare events with the weighted ensemble algorithm.Journal of computational chemistry · 2023Article
- Article
- Weighted ensemble: Recent mathematical developments.The Journal of chemical physics · 2023Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
As most relevant motions in biomolecular systems are inaccessible to conventional molecular dynamics simulations, algorithms that enhance sampling of rare events are indispensable. Increasing interest in intrinsically disordered systems and the desire to target ensembles of protein conformations (rather than single structures) in drug development motivate the need for enhanced sampling algorithms that are not limited to "two-basin" problems, and can efficiently determine structural ensembles. For systems that are not well-studied, this must often be done with little or no information about the dynamics of interest. Here we present a novel strategy to determine structural ensembles that uses dynamically defined sampling regions that are organized in a hierarchical framework. It is based on the weighted ensemble algorithm, where an ensemble of copies of the system ("replicas") is directed to new regions of configuration space through merging and cloning operations. The sampling hierarchy allows for a large number of regions to be defined, while using only a small number of replicas that can be balanced over multiple length scales. We demonstrate this algorithm on two model systems that are analytically solvable and examine the 10-residue peptide chignolin in explicit solvent. The latter system is analyzed using a configuration space network, and novel hydrogen bonds are found that facilitate folding.
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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.