BUDE - Bristol University Docking Engine

Principal Investigator: 

Simon McIntosh-Smith
simonm@compsci.bristol.ac.uk

Other application users/developers: 

University of Bristol – School of Biochemistry

Scientific area: 
Molecular Docking
Abstract: 
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.
Scalability: 
Good scaling up to thousands of GPU cores on SMP clusters or similar hybrid computing architectures.
Versions: 
OpenMP
CUDA
OpenCL
Other: 
C++ language
Tested on platforms: 

SMP cluster based on NVIDIA, AMD GPU, ARM CPUs and Mali GPUs, Intel Xeon Phi and Xeon processors.

Images: 
Any other information: 

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

More information: http://hpc.sagepub.com/content/early/2014/05/13/1094342014528252