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	MD3DOCKxb: A deep parallel optimized software for molecular docking with Intel Xeon Phi coprocessors
	Cheng, Qian2; Peng, Shaoliang2; Lu, Yutong2; Wu, Chengkun2; Wang, Haiqiang2; Liu, Xin2; Zhu, Weiliang1; Xu, Zhijian1; Zhang, Xinben1
	2015-07-07
DOI	10.1109/CCGrid.2015.64
页码	725-728
英文摘要	Molecular docking is a time consuming process, and it requires a substantial amount of computing power. D3DOCkxb was developed for investigating the effects of halogen bond in drug discovery by adding two precise score functions to Auto Dock. The docking accuracy of D3DOCkxb is better than Auto Dock, which can be attributed to a more complicated processing logic of D3DOCkxb. Consequently, it is an even more challenging task to do parallel optimization on D3DOCkxb. In this paper, we developed mD3DOCkxb, a MIC enabled version of D3DOCkxb, which utilizes Intel Xeon Phi, a Many-Integrated Core (MIC) accelerator, to boost the docking performance. We parallelized the Lamarckian Genetic Algorithm (LGA) in D3DOCKxb with OpenMP and port it to MIC with a number of optimization. And 12x to 18x speedup can be achieved, depending on the number of LGA iterations.
会议录	Proceedings - 2015 IEEE/ACM 15th International Symposium on Cluster, Cloud, and Grid Computing, CCGrid 2015
会议录出版者	Institute of Electrical and Electronics Engineers Inc.
文献子类	Proceedings Paper
语种	英语
内容类型	会议论文
源URL	[http://119.78.100.183/handle/2S10ELR8/266851]
专题	药物发现与设计中心
通讯作者	Peng, Shaoliang
作者单位	1.Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China 2.School of Computer Science, National University of Defense Technology, Changsha, China;
推荐引用方式 GB/T 7714	Cheng, Qian,Peng, Shaoliang,Lu, Yutong,et al. MD3DOCKxb: A deep parallel optimized software for molecular docking with Intel Xeon Phi coprocessors[C]. 见:.

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