Rigid Molecule Docking: FPGA Reconfiguration for Alternative Force

Molecular docking is one of the primary computational methods used by pharmaceutical companies to try to reduce the cost of drug discovery. A common docking technique, used for low-resolution screening or as an intermediate step, performs a three-dimensional correlation between two molecules to test for favorable interactions between them. We extend our previous work on FPGA-based docking accelerators, using reconfigurability for customization of the physical laws and geometric models that describe molecule interaction. Our approach, based on direct summation, allows straightforward combination of multiple forces and enables nonlinear force models; the latter, in particular, are incompatible with the transform-based techniques typically used. Our approach has the further advantage of supporting spatially oriented values in molecule models, as well as the detection of multiple positions representing favorable interactions. We report performance measurements on several different models of chemical behavior and show speedups of from 130 × to 1100 × over a PC. Copyright © 2006 Hindawi Publishing Corporation. All rights reserved. 1