Published March 26, 2025 | Version 2.0.0
Data paper Open

Moldrug algorithm for an automated ligand binding site exploration by 3D aware molecular enumerations (SI)

Authors/Creators

  • 1. ROR icon Saarland University
  • 2. Boehringer Ingelheim Pharma GmbH & Co KG, Medicinal Chemistry, Birkendorfer Str. 65, 88397 Biberach an der Riss, Germany
  • 3. Open Free Energy, Open Molecular Software Foundation, Davis, CA, 95616, United States

Description

Supporting informaiton for the paper Moldrug algorithm for an automated ligand binding site exploration by 3D aware molecular enumerations

Here are uploaded all files, instructions and data to reproduce the results (including images and analysis) of the paper.

Installation of the environment

conda create -n moldrug-paper python="3.9" ipykernel ipython ipywidgets -y
conda activate moldrug-paper
pip install moldrug
pip install -r https://raw.githubusercontent.com/ale94mleon/moldrug/refs/heads/main/streamlit/requirements.txt

Extra requirements


pip install pdb2pqr
pip install git+https://github.com/PatWalters/rd_filters.git

To follow the Notebooks in ./ref-crystals you need to install ADFRsuite. So you can use the script prepare_receptor.

Repo structure

  • 6lu7: It has both moldrug campaigns: configuration files and results.
  • figures-and-analysis: All the IPython-Notebooks to reproduce the images and analysis
  • full-data: A CSV (separated by ";") with all the data for the final population of generations 20; 45; 85; 100 (final populaiton of each stage).
  • mappers: JSON files with that map names internally used and moldrug IDX.

Files

zenodo-repo-moldrug-api-paper.zip

Files (21.9 MB)

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md5:f458d1e47cae827643fa4c064f16c255
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Additional details

Software

Repository URL
https://github.com/ale94mleon/moldrug
Programming language
Python