Other application users/developers:
University of Bristol – School of Biochemistry
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 at the University of Bristol. These energies approximate binding free energies in units of kJ/mol and are used both for pose and affinity prediction. The force-field 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.
Good scaling up to thousands of GPU cores on SMP clusters or similar hybrid computing architectures.