Data for Ligand Dissociation Pathways from Membrane Receptors Revealed by Weighted Ensemble Simulations

Description

We applied the weighted ensemble method (WE), an enhanced sampling method, in molecular dynamics (MD) simulations to sample the dissociation pathways of Norepinephrine (NE) and Epinephrine (EP) from β₁AR and β₂AR (membrane receptors). To analyze and visualize the results, we used machine learning-based techniques, such as principal component analysis (PCA), t-distributed stochastic neighbor embedding (t-SNE), and density-based spatial clustering of applications with noise (DBSCAN). We found that NE and EP dissociate via front-side pathways in β₁AR but favor a back-side pathway in β₂AR. WE simulations could yield reasonable koff values. The data set include all the necessary input files for running WE simulations and analysis the simulation results. The link for this data set will be shared in the corresponding paper that will be published.

Institutions

• University of California Davis

  CA, Davis
• University of North Texas

  TX, Denton

Categories

Funders

• American Heart Association

  Texas, United States

  Grant ID: 25CDA1450133
• American Heart Association

  Texas, United States

  Grant ID: 24POST1187017

Licence