The Performance of a Molecular Dynamics Simulation for the Plasmodium falciparum Enoyl-acyl carrier-protein Reductase Enzyme using Amber and GTX 780 and 970 Double Graphical Processing Units

Heru Suhartanto; Arry Yanuar; Ari Wibisono; Denny Hermawan; Alhadi Bustamam

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The Performance of a Molecular Dynamics Simulation for the Plasmodium falciparum Enoyl-acyl carrier-protein Reductase Enzyme using Amber and GTX 780 and 970 Double Graphical Processing Units

机译：使用琥珀色和GTX 780和970双图形处理单元对恶性疟原虫烯酰基-酰基载体-蛋白质还原酶进行分子动力学模拟的性能

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The invention of graphical processing units (GPUs) has significantly improved the speed of long processes used in molecular dynamics (MD) to search for drug candidates to treat diseases, such as malaria. Previous work using a single GTX GPU showed considerable improvement compared to GPUs run in a cluster environment. In the current work, AMBER and dual GTX 780 and 970 GPUs were used to run an MD simulation on the Plasmodium falciparum enoyl-acyl carrier protein reductase enzyme; the results showed that performance was improved, particularly for molecules with a large number of atoms using single GPU.

机译：图形处理单元（GPU）的发明显着提高了分子动力学（MD）中用于寻找治疗疟疾等疾病的候选药物的长过程的速度。与在集群环境中运行的GPU相比，以前使用单个GTX GPU的工作显示出了很大的改进。在当前的工作中，使用AMBER和双GTX 780和970 GPU在恶性疟原虫烯酰基-酰基载体蛋白还原酶上进行MD模拟。结果表明，性能得到了改善，特别是对于使用单个GPU的具有大量原子的分子而言。

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《International Journal of Technology》 |2018年第1期|共页
作者
Heru Suhartanto; Arry Yanuar; Ari Wibisono; Denny Hermawan; Alhadi Bustamam;
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中图分类一般工业技术;
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GPUMolecular dynamic simulationPfENR;

机译：GPU分子动态模拟;

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1. Molecular modeling studies, synthesis, and biological evaluation of Plasmodium falciparum enoyl-acyl carrier protein reductase (PfENR) inhibitors [J] . Varun A. Morde, Mushtaque S. Shaikh, Raghuvir R. S. Pissurlenkar, Molecular Diversity . 2009,第4期

机译：恶性疟原虫烯酰基-酰基载体蛋白还原酶（PfENR）抑制剂的分子建模研究，合成和生物学评估
2. Molecular modeling studies, synthesis, and biological evaluation of Plasmodium falciparum enoyl-acyl carrier protein reductase (PfENR) inhibitors [J] . Morde VA, Shaikh MS, Pissurlenkar RRS, Molecular diversity . 2009,第4期

机译：恶性疟原虫烯酰基-酰基载体蛋白还原酶（PfENR）抑制剂的分子建模研究，合成和生物学评估
3. Structural, dynamic, and electrostatic properties of fully hydrated DMPC bilayers from molecular dynamics simulations accelerated with graphical processing units (GPUs) [J] . Ganesan N., Bauer B.A., Lucas T.R., Journal of Computational Chemistry: Organic, Inorganic, Physical, Biological . 2011,第14期

机译：通过图形处理单元（GPU）加速的分子动力学模拟，充分水合的DMPC双层的结构，动态和静电特性
4. CHARACTERIZATION OF COARSE GRAIN MOLECULAR DYNAMIC SIMULATION PERFORMANCE ON GRAPHIC PROCESSING UNIT ARCHITECTURES [C] . Ardita Shkurti, Andrea Acquaviva, Elisa Ficarra, International Conference on Bioinformatics Models, Methods and Algorithms . 2012

机译：图形处理单元架构粗晶分子动态仿真性能的表征
5. Structural Dynamic and Electrostatic Properties of Fully Hydrated DMPC Bilayers From Molecular Dynamics Simulations Accelerated with Graphical Processing Units (GPUs) [O] . Narayan Ganesan, Brad A. Bauer, Timothy R. Lucas, -1

机译：与图形处理单元加速完全水化的DmpC双层膜的分子动力学模拟的结构动态和带电性能（图形处理器）
6. Enzyme Mechanism and Slow-Onset Inhibition of Plasmodium falciparum Enoyl-Acyl Carrier Protein Reductase by an Inorganic Complex [O] . de Medeiros, Patrícia Soares de Maria, Ducati, Rodrigo Gay, Basso, Luiz Augusto, 2011

机译：无机复合物的恶性疟原虫烯酰基-酰基载体蛋白还原酶的酶机制和缓慢抑制
7. Molecular Dynamics Simulation of Interfacial Electrochemical Processes: ElectricDouble Layer Screening [R] . Philpott, M. R., Glosli, J. N. 1996

机译：界面电化学过程的分子动力学模拟：电双层筛选

The Performance of a Molecular Dynamics Simulation for the Plasmodium falciparum Enoyl-acyl carrier-protein Reductase Enzyme using Amber and GTX 780 and 970 Double Graphical Processing Units

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