Published August 16, 2023 | Version 1

Supplementary information: How robust is the ligand binding transition state?

  • 1. Michigan State University

Description

We have used the REVO weighted ensemble approach followed by Markov state models to identify the ligand unbinding transition states for five ligands unbinding from the enzyme soluble epoxide hydrolase (sEH). This repo provides the counts matrices, properties and state (cluster) labels of the markov state models. The counts matrices can be converted to conformation space networks using CSNAnalysis software (https://github.com/ADicksonLab/CSNAnalysis). The networks are also provided in the gexf formatted files to be visualized in gephi (https://github.com/gephi/gephi).

Files

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Additional details

Funding

National Institutes of Health
Revealing the Ligand Binding Landscape with Advanced Molecular Simulation Methods 1R01GM130794-01