Molecular dynamics simulation data and analysis workflow for studying bivalent ligand binding to the guanidine-ii riboswitch

Abstract: The underlying study focused on ligand binding of bivalent ligands to the guanidine-II riboswitch. The dataset was generated using MD simulations and Machine Learning (ML) algorithms and contains the following directories and data: 1. simulation_data: Molecular Dynamics (MD) simulation trajectory data to replicate the analysis presented in the associated publication. 2. processed_data: Python code, a Python coding environment file, and a processed data file to replicate the dimensionality reduction and clustering workflow used in the associated publication. 3. sim_prep_example: Setup data and force field files to replicate the corresponding MD simulation data. See the README file for a more detailed description of content and technical instructions for this dataset.