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

doi:doi:10.48606/fTBvhsaGfoDmhOTV

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.

BibTex:

@dataset{Steuer_Jakob_2024,
    abstract = {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. },
    author = {Steuer, Jakob},
    doi = {10.48606/fTBvhsaGfoDmhOTV},
    institution = {RADAR},
    keyword = {'Clustering', 'Dimensionality Reduction', 'Guanidinium', 'Ligand Binding', 'MD Simulation', 'Machine Learning', 'Molecular Dynamics', 'RNA', 'Riboswitch', 'in vivo study'},
    title = {Molecular dynamics simulation data and analysis workflow for studying bivalent ligand binding to the guanidine-ii riboswitch},
    url = {https://service.tib.eu/ldmservice/vdataset/rdr-doi-10-48606-ftbvhsagfodmhotv},
    year = {2024}
}