ArticleLiving journal of computational molecular science2019
A Suite of Tutorials for the WESTPA Rare-Events Sampling Software [Article v1.0].
Article in Living journal of computational molecular science, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 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.
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The trial behind it
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Who cites it
19 citing papers in PubMed.
- 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
- Weighted Ensemble Simulations With the Drude Polarizable Model.Journal of computational chemistry · 2025Article
- Detection of Putative Ligand Dissociation Pathways in Proteins Using Site-Identification by Ligand Competitive Saturation.Journal of chemical information and modeling · 2025Article
- Thermodynamic Interpolation: A Generative Approach to Molecular Thermodynamics and Kinetics.Journal of chemical theory and computation · 2025Article
- Molecular simulations reveal intricate coupling between agonist-bound β-adrenergic receptors and G protein.iScience · 2025Article
- Multiple Chaperone DnaK-FliC Flagellin Interactions are Required for Pseudomonas aeruginosa Flagellum Assembly and Indicate a New Function for DnaK.Microbial biotechnology · 2025Article
- Dynamic allostery in the peptide/MHC complex enables TCR neoantigen selectivity.Nature communications · 2025Article
- System size effects on the free energy landscapes from molecular dynamics of phase-separating bilayers.The Journal of chemical physics · 2024Article
- Dynamic allostery in the peptide/MHC complex enables TCR neoantigen selectivity.Research square · 2024Article
- Understanding the free-energy landscape of phase separation in lipid bilayers using molecular dynamics.Biophysical journal · 2023Article
- Understanding the Free Energy Landscape of Phase Separation in Lipid Bilayers using Molecular Dynamics.bioRxiv : the preprint server for biology · 2023Article
- Translocation of a single Arg[Formula: see text] peptide across a DOPC/DOPG(4:1) model membrane using the weighted ensemble method.Scientific reports · 2023Article
- A Suite of Tutorials for the WESTPA 2.0 Rare-Events Sampling Software [Article v2.0].Living journal of computational molecular science · 2023Article
- WESTPA 2.0: High-Performance Upgrades for Weighted Ensemble Simulations and Analysis of Longer-Timescale Applications.Journal of chemical theory and computation · 2022Article
- Gaussian-Accelerated Molecular Dynamics with the Weighted Ensemble Method: A Hybrid Method Improves Thermodynamic and Kinetic Sampling.Journal of chemical theory and computation · 2021Article
- Free Energy Analyses of Cell-Penetrating Peptides Using the Weighted Ensemble Method.Membranes · 2021Article
- A Possible Mechanism of Graphene Oxide to Enhance Thermostability of D-Psicose 3-Epimerase Revealed by Molecular Dynamics Simulations.International journal of molecular sciences · 2021Article
- A glycan gate controls opening of the SARS-CoV-2 spike protein.bioRxiv : the preprint server for biology · 2021Article
- A Minimal, Adaptive Binning Scheme for Weighted Ensemble Simulations.The journal of physical chemistry. A · 2021Article
Corrections and comments
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Authors and funding
14 authors.
Funding
Abstract
The weighted ensemble (WE) strategy has been demonstrated to be highly efficient in generating pathways and rate constants for rare events such as protein folding and protein binding using atomistic molecular dynamics simulations. Here we present five tutorials instructing users in the best practices for preparing, carrying out, and analyzing WE simulations for various applications using the WESTPA software. Users are expected to already have significant experience with running standard molecular dynamics simulations using the underlying dynamics engine of interest (e.g. Amber, Gromacs, OpenMM). The tutorials range from a molecular association process in explicit solvent to more complex processes such as host-guest association, peptide conformational sampling, and protein folding.
Identifiers
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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.