Tools for the DUDE-Z benchmark dataset

This repository contains the scripts needed to obtain the DUDE-Z benchmark dataset and use it to evaluate the performance of drug discovery algorithms.

Requirements

• pydock3>=0.1.0rc

Installation

To install the requirements, you can use pip:

pip install 'pydock3>=0.1.0rc'

Usage: DockOpt

To run dockopt on the DUDE-Z benchmark, first clone this repository and download the dataset:

git clone https://github.com/docking-org/dude-z-benchmark
cd dude-z-benchmark/
bash make_dataset.sh

To run a single target (e.g., AMPC), specify its name as an argument:

bash benchmark_dockopt.sh AMPC

To run on all DUDE-Z targets, run with no arguments:

bash benchmark_dockopt.sh