BFEE-Docking

Author: Haohao Fu (fhh2626@nankai.edu.cn, fhh2626@gmail.com)

Introduction

BFEE-Docking is an open-source companion platform to BFEE3 for automated structure-based drug discovery workflows. It integrates virtual screening, flexible redocking, MD preparation, MM-GBSA calculations, and BFEE3-based absolute binding free-energy calculations into a single graphical workflow.

Starting from a standard protein PDB file and a ligand database in SMI/SDF/MOL2 format, BFEE-Docking can automate many routine preparation steps, including protein cleaning, pH-dependent protonation-state assignment, ligand preprocessing, binding-site definition, docking/redocking, file-format conversion, and preparation of downstream MD or free-energy calculation files.

BFEE-Docking also interfaces with PyMOL, allowing users to visualize binding pockets, docking boxes, docked ligand conformations, and flexible residues during the workflow.

Main features:

• Automated protein and ligand preprocessing
• pH-dependent protonation-state handling
• Binding-site definition by blind docking, pocket prediction, co-crystallized ligand, or manual input
• Rigid docking and flexible redocking
• Support for DSDP, smina, AutoDock Vina, QVina2, QVinaW and GNINA
• PyMOL-based visualization of intermediate results
• Preparation of MD-ready files for OpenMM simulations
• Support for MM-GBSA calculations
• Connection to BFEE3 for absolute binding free-energy calculations

License

• Main code: GPL-3.0 or later

This distribution bundles third-party components. Each component remains under its own license. They are distributed as separate works by mere aggregation and are not relicensed by this project.

The bundled third-party programs, except the MIT-licensed pocketeer, are used as independent executables and are invoked via the command line. They are not linked into the main program, and no third-party source code is incorporated into the main codebase.

All third-party license texts are included in the licenses/ folder.

Bundled third-party components:

• OpenBabel 3.1.1 (binary): GPL-2.0
• smina 2020.12.10 (binary): Apache-2.0
• AutoDock Vina 1.2.7 (binary): Apache-2.0
• QuickVina-W/2 (binary): Apache-2.0
• DSDP-redocking (source code): Apache-2.0
• pocketeer (source code): MIT

Their source code corresponding to the bundled version:

• OpenBabel 3.1.1: https://github.com/openbabel/openbabel/releases/tag/openbabel-3-1-1
• smina 2020.12.10: https://github.com/jaimergp/smina/releases/tag/2020.12.10
• AutoDock Vina 1.2.7: https://github.com/ccsb-scripps/AutoDock-Vina/releases/tag/v1.2.7
• QuickVina-W/2: https://github.com/QVina/qvina
• DSDP-redocking: https://github.com/PKUGaoGroup/DSDP
• pocketeer: https://github.com/cch1999/pocketeer

Installation and Usage

pip install bfee-docking

For servers running GPU-based docking, unzip third_party/DSDP_redocking.zip and enter the DSDP folder. Then type:

make

For servers running MD simulations:

pip install parmed mdanalysis
pip install "openmm[cuda13]>=8.5"