Parallel implementation of AutoDock
Parallel implementation of AutoDock
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DOI：
10.1107/s0021889807011053
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发表时间：
2007-06-01
影响因子：
6.1
通讯作者：
Govindarajan, R.
中科院分区：
文献类型：
--
作者：
Khodade, Prashant;Prabhu, R.;Govindarajan, R.
配基与蛋白质结构的计算对接是基于结构的药物设计的关键步骤。目前，每次对接所需的时间很长，因此限制了对接以高吞吐量的方式使用，这就保证了对接算法的并行化。AutoDock是一种广泛使用的工具，已被选为并行化工具。在96个处理器上观察到近乎线性的速度增长，例如，在单个IBM Power-5处理器(1.65 GHz)上，将配体对接到艾滋病毒蛋白酶所需的时间从81分钟减少到大约1分钟，在具有96个这样的处理器的IBM集群上。这种实现将使使用AutoDock进行虚拟配体筛选变得可行。
Computational docking of ligands to protein structures is a key step in structure-based drug design. Currently, the time required for each docking run is high and thus limits the use of docking in a high-throughput manner, warranting parallelization of docking algorithms. AutoDock, a widely used tool, has been chosen for parallelization. Near-linear increases in speed were observed with 96 processors, reducing the time required for docking ligands to HIV-protease from 81 min, as an example, on a single IBM Power-5 processor ( 1.65 GHz), to about 1 min on an IBM cluster, with 96 such processors. This implementation would make it feasible to perform virtual ligand screening using AutoDock.