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A Parallel Molecular Docking Approach Based on Message Passing Interface

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5 Author(s)
Cun Xin Wang ; Coll. of Life Sci. & Bioeng., Beijing Univ. of Technol., Beijing ; Shan Chang ; Wei-zu Chen ; Xin-qi Gong
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Molecular docking technology is an important tool in computer-aided drug discovery and structure prediction for the protein-ligand complex. In this work, based on the analysis of the algorithm of the widely used the docking program AutoDock, we proposed a hybrid parallel method using the message passing interface (MPI) library. The modified programs were applied to dock the small molecule XK263 to its target HIV-1 protease with different number of processors. Docking results indicate that the parallel codes can make a good prediction of the XK263-protease complex structure. The obtained high quality parallel speedup and efficiency show the promising improvement of our method for future applications on structure prediction of protein complex and drug design.

Published in:

Pervasive Computing and Applications, 2008. ICPCA 2008. Third International Conference on  (Volume:2 )

Date of Conference:

6-8 Oct. 2008