Grid Enabled MPI (GEM) System:Toward Maximum Computational Efficiency in Molecular Docking and Virtual Screening

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Title:	Grid Enabled MPI (GEM) System:Toward Maximum Computational Efficiency in Molecular Docking and Virtual Screening
Authors:	Jui-Le Chen(陳瑞樂) Bor-Ruey Huang(黃博瑞) Kuan-Han Lee(李冠漢)
Contributors:	Department of Computer Science and lnformation Engineering Faculty of Medicinal and Applied Chemistry, Kaohsiung Medical University Department of Pharmacy, Tajen University
Keywords:	Grid Enabled MPI (GEM) System Gird Computing parallel computing molecular docking virtual screening
Date:	2008-07
Issue Date:	2017-12-04 15:55:10 (UTC+8)
Abstract:	The increasing economic pressure on the pharmaceutical industry to develop new drugs in faster and more efficient way than in the past has led to the development of a large number of new methods aimed at a more efficient and rapid lead structure discovery process. One of the key aspects of parallel computing is clusters using MPI that distributing a large computational task onto several machines. Another approach to get high computing power at low cost is grid computing. However, it would be very much attractive to integrate parallel and grid computing approaches in achieving the most effective solution. Here, we describe Grid Enabled MPI (GEM) System that integrates individual clusters at different geographic locations as grid nodes for virtual screening. In GEM System, each node will be a single host or a cluster with its own parallel processing environment with MPI interface. The efficiency of GEM System was evaluated by molecules docking. All 5,000 compounds were screened within UCSF DOCK. It took about 1,357,914 seconds in standalone mode and 87,626 seconds on 20 nodes GEM system, respectively.
Relation:	第五屆海峽化學、生物及材料研討會，起迄日：2008/07/21-2008/07/22，地點：嘉南藥理科技大學
Appears in Collections:	[Pharmacy and Science] The 5rh Conference of Channel-bridge Chemistry, Biology and materal Science

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