Publication details

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



Year of publication 2009
Type Article in Proceedings
Conference MEMICS 2009: Fifth Doctoral Workshop on Mathematical and Engineering Methods in Computer Science
MU Faculty or unit

Faculty of Science

Field Informatics
Keywords molecular docking; autogrid; autodock; acceleration; GPU; high performance computing
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 the original AutoGrid more than $400\times$ for large, but quite common molecules and sufficiently large grids.
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