FPGA-based acceleration of the AutoDock molecular docking software

AutoDock is a popular software for the bioinformatics related molecular docking problem. The FPGA-based acceleration of AutoDock is presented and evaluated in this paper. The implementation applies pipelines and fine-grained parallelization, and achieves a ×10-40 speedup over a 3.2 GHz CPU. Test runs show that the overall accuracy of the algorithm was preserved despite the slight modifications of the original method and the fixed-point arithmetic used in the FPGA.