ArticleACS omega2020
Wepy: A Flexible Software Framework for Simulating Rare Events with Weighted Ensemble Resampling.
Article in ACS omega, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
- Assessing the Stability of Molecular Glues with Weighted Ensemble Simulations.Journal of chemical theory and computation · 2026Article
- Hold on tight: the kinetic profiling of opioid receptor ligands using the CORAL-MD.Journal of cheminformatics · 2026Article
- Residence time in drug discovery: current insights and future perspectives.Pharmacological reports : PR · 2025Review
- Markov State Models with Weighted Ensemble Simulation: How to Eliminate the Trajectory Merging Bias.Journal of chemical theory and computation · 2025Article
- Dietary flavonoids form supramolecular assemblies, alter biochemistry, and enhance cell resilience.Frontiers in nutrition · 2025Article
- BAD-NEUS: Rapidly converging trajectory stratification.The Journal of chemical physics · 2024Article
- Ligand Gaussian Accelerated Molecular Dynamics 3 (LiGaMD3): Improved Calculations of Binding Thermodynamics and Kinetics of Both Small Molecules and Flexible Peptides.Journal of chemical theory and computation · 2024Article
- Ligand Gaussian accelerated Molecular Dynamics 3 (LiGaMD3): Improved Calculations of Binding Thermodynamics and Kinetics of Both Small Molecules and Flexible Peptides.bioRxiv : the preprint server for biology · 2024Article
- Article
- How Robust Is the Ligand Binding Transition State?Journal of the American Chemical Society · 2023Article
- SOURSOP: A Python Package for the Analysis of Simulations of Intrinsically Disordered Proteins.Journal of chemical theory and computation · 2023Article
- Predicting Biomolecular Binding Kinetics: A Review.Journal of chemical theory and computation · 2023Review
- Quality over quantity: Sampling high probability rare events with the weighted ensemble algorithm.Journal of computational chemistry · 2023Article
- Ligand Gaussian Accelerated Molecular Dynamics 2 (LiGaMD2): Improved Calculations of Ligand Binding Thermodynamics and Kinetics with Closed Protein Pocket.Journal of chemical theory and computation · 2023Article
- Adrenomedullin 2/intermedin is a slow off-rate, long-acting endogenous agonist of the adrenomedullinbioRxiv : the preprint server for biology · 2023Article
- Weighted ensemble: Recent mathematical developments.The Journal of chemical physics · 2023Article
- CHARMM-GUI Implicit Solvent Modeler for Various Generalized Born Models in Different Simulation Programs.The journal of physical chemistry. B · 2022Article
- Single-molecule studies reveal method for tuning the heterogeneous activity of alkaline phosphatase.Biophysical journal · 2022Article
- WESTPA 2.0: High-Performance Upgrades for Weighted Ensemble Simulations and Analysis of Longer-Timescale Applications.Journal of chemical theory and computation · 2022Article
- Local Ion Densities can Influence Transition Paths of Molecular Binding.Frontiers in molecular biosciences · 2022Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
Here, we introduce the open-source software framework wepy (https://github.com/ADicksonLab/wepy) which is a toolkit for running and analyzing weighted ensemble (WE) simulations. The wepy toolkit is in pure Python and as such is highly portable and extensible, making it an excellent platform to develop and use new WE resampling algorithms such as WExplore, REVO, and others while leveraging the entire Python ecosystem. In addition, wepy simplifies WE-specific analyses by defining out-of-core tree-like data structures using the cross-platform HDF5 file format. In this paper, we discuss the motivations and challenges for simulating rare events in biomolecular systems. As has previously been shown, high-dimensional WE resampling algorithms such as WExplore and REVO have been successful at these tasks, especially for rare events that are difficult to describe by one or two collective variables. We explain in detail how wepy facilitates implementation of these algorithms, as well as aids in analyzing the unique structure of WE simulation results. To explain how wepy and WE work in general, we describe the mathematical formalism of WE, an overview of the architecture of wepy, and provide code examples of how to construct, run, and analyze simulation results for a protein-ligand system (T4 Lysozyme in an implicit solvent). This paper is written with a variety of readers in mind, including (1) those curious about how to leverage WE rare-event simulations for their domain, (2) current WE users who want to begin using new high-dimensional resamplers such as WExplore and REVO, and (3) expert users who would like to prototype or implement their own algorithms that can be easily adopted by others.
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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.