Supplementary Data for the Paper 'Moltiverse: Molecular Conformer Generation Using Enhanced Sampling Methods'
Creators: name: Bedoya, Mauricio
name: Adasme Carreño, Francisco
name: Peña-Martínez, Paula Andrea
name: Muñoz-Gutiérrez, Camila
name: Peña-Tejo, Luciano
name: Márquez-Montesinos, José C. E.
name: Hernández-Rodríguez, Erix W.
name: González, Wendy
name: Martinez, Leandro
name: Alzate-Morales, Jans
Publisher: name: figshare
Year: 2024
Subjects: classificationCode: 340701
subject: Computational chemistry
classificationCode: 310201
subject: Bioinformatic methods development

description: The Moltiverse code is hosted on GitHub at: https://github.com/ucm-lbqc/moltiverseDataset Structure:1. Cofactorv1 Dataset (cofactor_v1_dataset/). This folder contains two types of subfolders for each cofactor:*_original/: Raw files extracted directly from PDB files*_rearranged_atoms/: Files processed by RDKit and chem.cr for homogeneous atom arrangement to facilitate RMSD calculations. The cofactorv1 dataset contains 8412 experimental structures extracted from the PDB.2. Input scripts (input_scripts). This folder contains essential scripts for: performance benchmarking, time measurement analysis and SMI file processing. Replace the variables accordingly.3. Time performance (time_performance). This folder contains tools and results for performance evaluation.4. Analysis Data (moltiverse_v1_data/). Contains raw data, analysis notebooks, and statistical results.Raw data files: energy, rdgyr, rmsd_matrix, rmsd_minAnalysis notebooks: ipynb notebooksstatistics_r/: Processed data and statistical analysis subfoldersAnalysis WorkflowStep 1: Data Export and Initial AnalysisA1_export_data_to_statistics_r.ipynbA2_plots_data_and_analysis.ipynbStep 2: Statistical ProcessingRun R Markdown scripts (.Rmd) in sequence from folders 01 through 08 in statistics_r/Step 3: Visualization and PlottingB1_plots_statistics_matrix.ipynbB2_plots_linear.ipynbB3_plots_spider.ipynbStep 4: Statistics by Replica AnalysisRun C1_plots_statistics_matrix_per_replica.ipynb in the 08_statistics_by_replica/ folder.Larger files with analysis results are distributed in three ZIP archives for easy handling. Each archive contains specific sets of analyses:moltiverse_v1_data_A.zipmoltiverse_v1_data_B.zipmoltiverse_v1_data_C.zip<i>Notes: All paths are relative to the repository root. </i><i>Execute notebooks and scripts in the specified order to ensure proper data flow. </i><i>Ensure all dependencies are installed before running the analysis pipeline.</i>Attribution and License InformationThis project includes and modifies code from:"High-Quality Conformer Generation with CONFORGE: Algorithm and Performance Assessment" Thomas Seidel, Christian Permann, Oliver Wieder, Stefan M. Kohlbacher, and Thierry Langer; Journal of Chemical Information and Modeling. 2023 63 (17), 5549-5570DOI: 10.1021/acs.jcim.3c00563<br>SUPPLEMENTARY DATA - DOI: 10.5281/zenodo.8137603Original Authors: Seidel, Thomas, Permann, Christian, Wieder, Oliver, Kohlbacher, Stefan Michael, Langer, ThierryOriginal Release Date: 2023Modifications: Some scripts (input_scripts) have been modified from their original versions by Mauricio Bedoya.Modifications include: Code reformatting, and restructured execution workflow to reduce dependency on auxiliary bash scripts.Modified files are marked with appropriate headers indicating license attribution.License InformationOriginal License: GPLv2Current License: GPLv2Date of License Update: 2024Proper CitationIf you use these scripts, please cite:"High-Quality Conformer Generation with CONFORGE: Algorithm and Performance Assessment" Thomas Seidel, Christian Permann, Oliver Wieder, Stefan M. Kohlbacher, and Thierry Langer; Journal of Chemical Information and Modeling. 2023 63 (17), 5549-5570DOI: 10.1021/acs.jcim.3c00563<br>Seidel, T., Permann, C., Wieder, O., Kohlbacher, S. M., &amp; Langer, T. (2023). Supplementary Data for the Paper 'High-Quality Conformer Generation with CONFORGE: Algorithm and Performance Assessment'. https://doi.org/10.5281/zenodo.8137603<br>Also cite this current repository and Moltiverse work (Check citation section at GitHub): https://github.com/ucm-lbqc/moltiverse