UniDock‑Pro

UniDock‑Pro is an all‑in‑one GPU‑accelerated virtual screening platform. It provides classical docking, ligand similarity searching, and hybrid docking in a single binary.

Project lineage. UniDock‑Pro is a fork of Uni‑Dock, which is a GPU-accelerated version of AutoDock-Vina. Please also see the Uni‑Dock publication: DOI: 10.1021/acs.jctc.2c01145.

Citation & Preprint

If you use UniDock‑Pro in academic work, please cite the Uni‑Dock paper above and our JCIM paper:

• UniDock‑Pro: https://pubs.acs.org/doi/full/10.1021/acs.jcim.5c02587

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Building from source

1. Install dependencies

   • CUDA Toolkit ≥ 11.8 — follow NVIDIA’s installation guide.

   • CMake ≥ 3.16

   • C++ compiler (must be compatible with NVCC; g++ works in most cases)

   • Boost ≥ 1.72

     sudo apt install \
       libboost-system-dev libboost-thread-dev libboost-serialization-dev \
       libboost-filesystem-dev libboost-program-options-dev libboost-timer-dev

     If the above does not satisfy version requirements, install from Boost source or via Anaconda: conda install -c anaconda libboost.

2. Clone the repository

   git clone https://github.com/NiBoyang/UniDock-Pro.git

3. Build with CMake

   cd UniDock-Pro
   cmake -B build
   cmake --build build -j4

The main binary udp will be generated under build/.

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Usage

Run ./udp --help for the full set of options. Minimal, reproducible examples are shown below.

Required option — --search_mode. You must explicitly set --search_mode to one of fast, balance, or detail. Leaving it unset is currently unsupported and may lead to incorrect or unstable behavior.

Input expectations

• Receptor: .pdbqt
• Ligands: Two input methods are supported:
  • A text file (--ligand_index) listing .pdbqt paths, one per line
  • A directory (--ligand_directory) containing .pdbqt files
• Reference ligand(s) (for similarity searching or hybrid docking):
  • Single reference: --reference_ligand ref.pdbqt
  • Multiple references (ensemble): --reference_ligand ref1.pdbqt ref2.pdbqt ref3.pdbqt (space-separated)
• Search box: --center_{x,y,z} and --size_{x,y,z} in Å
• Output directory (optional): --dir <path>

Classical docking

Using a ligand index file:

./udp \
  --receptor rec.pdbqt \
  --ligand_index ligand_index.txt \
  --center_x 0 --center_y 0 --center_z 0 \
  --size_x 20 --size_y 20 --size_z 20 \
  --search_mode balance \
  --dir ./results

Using a ligand directory:

./udp \
  --receptor rec.pdbqt \
  --ligand_directory ./ligands/ \
  --center_x 0 --center_y 0 --center_z 0 \
  --size_x 20 --size_y 20 --size_z 20 \
  --search_mode balance \
  --dir ./results

Ligand similarity searching

With a single reference ligand:

./udp \
  --reference_ligand ref.pdbqt \
  --ligand_index ligand_index.txt \
  --center_x 0 --center_y 0 --center_z 0 \
  --size_x 20 --size_y 20 --size_z 20 \
  --search_mode fast \
  --dir ./results

With multiple reference ligands (ensemble):

./udp \
  --reference_ligand ref1.pdbqt ref2.pdbqt ref3.pdbqt \
  --ligand_index ligand_index.txt \
  --center_x 0 --center_y 0 --center_z 0 \
  --size_x 20 --size_y 20 --size_z 20 \
  --search_mode fast \
  --dir ./results

Hybrid docking

Important: In hybrid mode, the --reference_ligand must be provided in its co‑crystallized pose with the specified receptor.

With a single reference ligand:

./udp \
  --receptor rec.pdbqt \
  --reference_ligand ref.pdbqt \
  --ligand_index ligand_index.txt \
  --center_x 0 --center_y 0 --center_z 0 \
  --size_x 20 --size_y 20 --size_z 20 \
  --search_mode detail \
  --dir ./results

With multiple reference ligands (ensemble):

./udp \
  --receptor rec.pdbqt \
  --reference_ligand ref1.pdbqt ref2.pdbqt ref3.pdbqt \
  --ligand_index ligand_index.txt \
  --center_x 0 --center_y 0 --center_z 0 \
  --size_x 20 --size_y 20 --size_z 20 \
  --search_mode detail \
  --dir ./results

Worked example (from the example/ folder)

From the repository’s example/ directory:

  ../build/udp \
  --receptor ./receptor/rec.pdbqt \
  --reference_ligand ./ref_lig/xtal_lig.pdbqt \
  --ligand_index ligand_index.txt \
  --center_x 32.790 --center_y 38.342 --center_z 58.486 \
  --size_x 28 --size_y 28 --size_z 28 \
  --search_mode balance \
  --dir ./results

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Acknowledgements

UniDock‑Pro builds on the ideas and engineering of AutoDock Vina and the GPU‑accelerated Uni‑Dock project. We thank their authors and contributors for foundational work that enabled this fork.