Bude
Bristol University Docking Engine with ClearSpeed Acceleration
ClearSpeed acceleration of the Bristol University Docking Engine (Bude) algorithm has been shown to deliver a speedup of 4.5x compared with 2.8GHz Intel® Xeon® and AMD64 4600+based systems for compute intensive sections of the code using a single Advance X620 accelerator board. Up to 11x speedup has been achieved using multiple Advance X620 accelerators.
Bude is currently under development as a generic molecular docking program under the direction of Dr. Richard Sessions and Prof. Anthony Clarke of the Bristol Protein Folding Group.
The user provides the receptor and ligand start positions and defines a 6 dimensional search grid (based on the 3 possible translational and 3 rotational degrees of freedom in Cartesian space). This grid is searched via a GA-like EMC (Evolutionary Monte Carlo) procedure analogous to that described for internal degrees of freedom in the RAFT peptide folding algorithm (N. Gibbs, A.R. Clarke & R.B. Sessions, "Ab-initio Protein Folding using Physicochemical Potentials and a Simplified Off-Lattice Model", Proteins 43:186-202,2001). Flexibility in the ligand is provided via specified torsional bond freedom. This functionality will also be added to the receptor, which is currently treated as rigid. The algorithm is implemented in both FORTRAN and C++. The force field employed for assessing each pose is a heavy-atom based soft-core potential model, derived from the RAFT force field with additional electrostatic terms.
Acceleration of this algorithm has been obtained on the ClearSpeed Advance X620 accelerator board by porting the energy calculation and geometry routines to the ClearSpeed Advance accelerator.
| 1 CPU, no acceleration | 48.2 seconds |
| 1 Advance X620 board | 10.6 seconds, 4.5x speedup |
| 2 Advance X620 | 5.8 seconds, 8.3x speedup |
| 3 Advance X620 boards | 4.4 seconds, 11.0x speedup |
Host: 2 x 2.8 GHz Xeon, OS RHEL4-64, CSXL version 2.24