Codes for Zhou, G., Rusnac, DV., Park, H. et al. An artificial intelligence accelerated virtual screening platform for drug discovery. Nat Commun 15, 7761 (2024). https://doi.org/10.1038/s41467-024-52061-7
Software installation time is less than 2 hours on a regular desktop
Please follow the instructions in https://github.com/RosettaCommons/rosetta.
After the installation, run export ROSETTAHOME=your_local_path, remember to replace your_local_path with your the actual installation path.
Please follow the instructions in https://github.com/durrantlab/dimorphite_dl.
After the installation, run export DIMORPHITE=your_local_path, remember to replace your_local_path with your the actual installation path.
conda create -n openvs python=3.9
conda install --file requirements.txt
conda install pytorch torchvision torchaudio pytorch-cuda=12.1 -c pytorch -c nvidia
pip install -e .
To install the CSD Python API, follow the instructions at this link. Due to potential package conflicts, please install it in a separate conda environment. The CSD Python API is only needed during the post-docking analysis. Specifically, only geometry_analysis.py requires the CSD Python API.
The drug-like centroid library can be downloaded at: https://files.ipd.uw.edu/pub/OpenVS/centroids.tgz
ZINC22 3d can be downloaded from: https://cartblanche22.docking.org/
Enamine REAL library can be downloaded from: https://enamine.net/compound-collections/real-compounds/real-database
Once downloaded, put the library in ./databases
openvs folder contains utility modules for OpenVS platform
benchmarks folder contains scripts to run benchmarks on two datasets:
"benchmarks/casf_2016" CASF2016 benchmark
"benchmarks/casf_2016/eval_docking_cpp" Docking power. Please see README file in the folder for instructions.
"benchmarks/casf_2016/eval_screening_cpp" Sreening power. Please see README file in the folder for instructions.
"benchmarks/casf_2016/holo_relax_apo_cstw1" Folder contains constraint relaxed holo pdb file from CASF2016.
"benchmarks/casf_2016/params_new" Folder contains the params file for the ligands in CASF2016.
"benchmarks/dud" DUD benchmark
Please see README file in the folder for instructions.
experiments folder contains two virtual screning experiments performed in this work
Please see the README file in the folder for instructions.
databases folder contains example small molecule database files
scripts folder contains scripts to preprocess and generate fingerprints for the small molecules in the database.