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  2. Molecular Dynamics Simulation Data and Analysis Workflow for Studying Bivalent Ligand Binding to the Guanidine-II Riboswitch
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    Datenpaket: Molecular Dynamics Simulation Data and Analysis Workflow for Studying Bivalent Ligand Binding to the Guanidine-II Riboswitch

    Alternativer Identifier:
    -
    Verwandter Identifier:
    (Is Supplement To) 10.1093/nargab/lqae132 - DOI
    Ersteller/in:
    Beitragende:
    (Project Member)
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    Titel:
    Molecular Dynamics Simulation Data and Analysis Workflow for Studying Bivalent Ligand Binding to the Guanidine-II Riboswitch
    Weitere Titel:
    -
    Beschreibung:
    (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.
    Schlagworte:
    RNA
    Riboswitch
    Guanidinium
    MD Simulation
    Molecular Dynamics
    Ligand Binding
    in vivo study
    Machine Learning
    Clustering
    Dimensionality Reduction
    Zugehörige Informationen:
    -
    Sprache:
    Englisch
    Herausgeber/in:
    University of Konstanz
    Erstellungsjahr:
    Fachgebiet:
    Chemistry
    Objekttyp:
    (Dataset) Simulation Setup Files, Simulation Data, Jupyter Notebook
    Datenquelle:
    (Other) Molecular Dynamics Simulations
    Verwendete Software:
    Software für Datenerhebung
    Software:
    GROMACS - 2020.4
    Alternative Software:
    -
    Verwendete Software:
    Software für Datenbearbeitung
    Software:
    EncoderMap - 1
    HDBSCAN - 0.8.19
    Alternative Software:
    -
    Datenverarbeitung:
    -
    Erscheinungsjahr:
    Rechteinhaber/in:
    Förderung:
    Deutsche Forschungsgemeinschaft (35/1134-1 FUGG)
    Konstanz Research School Chemical Biology
    Name Speichervolumen Metadaten Upload Aktion
    Status:
    Publiziert
    Eingestellt von:
    eb7a4111465b77dd5af1bd1102d924d6
    Erstellt am:
    Archivierungsdatum:
    2024-08-28
    Archivgröße:
    13,7 GB
    Archiversteller:
    00a5910a2b77a3793bbf250744b60665
    Archiv-Prüfsumme:
    59d55e4ae2b4ce742b2077b10b5a9ceb (MD5)
    Embargo-Zeitraum:
    -