Bristol University Docking Engine (BUDE)

BUDE is a general purpose molecular docking program written in C++, OpenMP and OpenCL that uses GPU acceleration to perform:

  1. Virtual screening by docking of millions of small-molecule ligands
  2. Ligand binding site identification on protein surfaces
  3. Protein-protein docking in real space

Interaction energies are calculated using an empirical free energy forcefield developed here. These energies approximate binding free energies in units of kJ/mol and are used both for pose and affinity prediction. The forcefield comprises very soft-core potentials to accommodate geometrical approximations inherent in the docking approach and is designed to give a better balance between energetic interactions and shape matching than more traditional methods.

Licence

The software is available free to academics and at modest cost to commercial organisations.

Academic User Agreement

Please contact Richard Sessions to obtain a copy of BUDE: R.Sessions@bristol.ac.uk

Authors:

Amaurys Avila Ibarra, James Price, Debbie Shoemark, Tony Clarke, Simon McIntosh-Smith, and Richard Sessions.

Contributors

References (PDF, 42.5kB)

BUDE has been compiled and run on x86 platforms under unix and linux with Nvidia and AMD GPUs, also Intel Xeon-Phi, and ARM processors. Requirements: C++ compiler; acceleration: OpenMP (Multicore), OpenCL (manycore).

BBSRC

Supported by the BBSRC