FastGrid -- The Accelerated AutoGrid Potential Maps Generation for Molecular Docking

Warning

This publication doesn't include Faculty of Economics and Administration. It includes Faculty of Informatics. Official publication website can be found on muni.cz.

Authors	OLŠÁK Marek FILIPOVIČ Jiří PROKOP Martin
Year of publication	2010
Type	Article in Periodical
Magazine / Source	Computing and Informatics
MU Faculty or unit	Faculty of Informatics
Citation
Field	Informatics
Keywords	acceleration; GPU; CUDA; AutoDock; AutoGrid
Description	The AutoDock suite is widely used molecular docking software consisting of two main programs -- AutoGrid for precomputation of potential grid maps and AutoDock for docking into potential grid maps. In this paper, the acceleration of potential maps generation based on AutoGrid and its implementation called FastGrid is presented. The most computationally expensive algorithms are accelerated using GPU, the rest of algorithms run on CPU with asymptotically lower time complexity that has been obtained using more sophisticated data structures than in the original AutoGrid code. Moreover, the CPU implementation is parallelized to fully exploit computational power of machines that are equipped with more CPU cores than GPUs. Our implementation outperforms original AutoGrid more than 400x for large, but quite common molecules and sufficiently large grids.
Related projects:	Proteins in metabolism and interaction of organisms with the environment Highly Parallel and Distributed Computing Systems Rozsáhlé výpočetní systémy: modely, aplikace a verifikace