Acceleration of a production rigid molecule docking code

Abstract

Modeling the interactions of biological molecules, or docking is critical to both understanding basic life processes and to designing new drugs. Here we describe the FPGA-based acceleration of a recently developed, complex, production docking code. We find that it is necessary to extend our previous 3D correlation structure in several ways, most significantly to support simultaneous computation of several correlation functions. The result is a hundred-fold speed-up of a section of the code that represents over 92% of the original run-time. An additional 4% is accelerated through a previously described method, yielding a total acceleration of almost 25times for typical protein-ligand combinations.