Title :
FPGA-based acceleration of the AutoDock molecular docking software
Author :
Pechan, Imre ; Fehér, Béla ; Bérces, Attila
Author_Institution :
Dept. of Meas. & Inf. Syst., Budapest Univ. of Technol. & Econ., Budapest, Hungary
Abstract :
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.
Keywords :
bioinformatics; field programmable gate arrays; fixed point arithmetic; molecular biophysics; parallel processing; AutoDock molecular docking software; FPGA-based acceleration; bioinformatics; fine-grained parallelization; fixed-point arithmetic; related molecular docking problem; Atomic clocks; Field programmable gate arrays; Pipelines; Prediction algorithms; Random access memory; Search methods; AutoDock; FPGA; bioinformatics; hardware acceleration; molecular docking;
Conference_Titel :
Ph.D. Research in Microelectronics and Electronics (PRIME), 2010 Conference on
Conference_Location :
Berlin
Print_ISBN :
978-1-4244-7905-4
