Automated molecular binding site exploration with Moldrug algorithm (SI)
Year: 2024
Type: article
Abstract: 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.
Authors: Martínez León, Alejandro, Ries, Benjamin, Hub, Jochen S., Magarkar, Aniket
Language: English
Subfield: Computational Theory and Mathematics
Field: Computer Science
Domain: Physical Sciences
Open Access status: green
OpenAlex ID: W6893086460
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