MEGADOCK-GPU : Acceleration of Protein-Protein Docking Calculation on GPUs
MEGADOCK-GPU : Acceleration of Protein-Protein Docking Calculation on GPUs
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MEGADOCK-GPU：GPU上蛋白质-蛋白质对接计算的加速
DOI：
10.1145/2506583.2506693
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发表时间：
2013
期刊：
影响因子：
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通讯作者：
Yutaka Akiyama
中科院分区：
文献类型：
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作者：
Takehiro Shimoda;Takashi lshida;Shuji Suzuki;Masahito Ohue;Yutaka Akiyama
蛋白质-蛋白质对接是一种从单体蛋白质结构预测蛋白质复合物结构的方法。由于蛋白质结构信息的不断增加以及应用领域的不断扩展，如相互作用体预测等，人们迫切需要一种快速的蛋白质-蛋白质对接方法。MEGADOCK是一款快速的蛋白质-蛋白质对接软件，但对于由数百万个蛋白质对组成的相互作用组预测，需要更多的加速。本文采用通用GPU计算技术开发了一个超快速蛋白质对接软件MEGADOCK-GPU。我们实现了一个利用计算节点中所有CPU内核和GPU的系统。结果，12个CPU核心和3个GPU上的MEGADOCK-GPU实现了比1个CPU核心上的MEGADOCK快37.0倍的计算速度。新的对接软件将促进对接技术的应用，以协助大规模的蛋白质相互作用网络分析。MEGADOCK-GPU可从http://www.bi.cs.titech.ac.jp/megadock/gpu/免费获得。
Protein-protein docking is a method for predicting the protein complex structure from monomeric protein structures. Because protein structural information has been increased and the application field has been expanded to more difficult ones such as interactome prediction, a faster protein-protein docking method has been eagerly demanded. MEGADOCK is fast protein-protein docking software but more acceleration is demanded for an interactome prediction, which is composed of millions of protein pairs. In this paper, we developed an ultra-fast protein-protein docking software named MEGADOCK-GPU by using general purpose GPU computing techniques. We implemented a system that utilizes all CPU cores and GPUs in a computation node. As results, MEGADOCK-GPU on 12 CPU cores and 3 GPUs achieved a calculation speed that was 37.0 times faster than MEGADOCK on 1 CPU core. The novel docking software will facilitate the application of docking techniques to assist large-scale protein interaction network analyses. MEGADOCK-GPU is freely available at http://www.bi.cs.titech.ac.jp/megadock/gpu/.