OpenVS

Codes for "An artificial intelligence accelerated virtual screening platform for drug discovery". [https://www.biorxiv.org/content/10.1101/2024.03.28.587262v1]

Installation

Software installation time is less than 2 hours on a regular desktop

Install Rosetta

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.

Install Dimorphite-DL 1.2.4

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.

Install OpenVS

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 CSD Python API, follow https://downloads.ccdc.cam.ac.uk/documentation/API/installation_notes.html

Small molecule library

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

Usage

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.

gfzhou / OpenVS