High-throughput calculation of protein-ligand binding affinities: Modification and adaptation of the MM-PBSA protocol to enterprise grid computing
High-throughput calculation of protein-ligand binding affinities: Modification and adaptation of the MM-PBSA protocol to enterprise grid computing
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DOI：
10.1021/ci050488t
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发表时间：
2006-05-01
影响因子：
5.6
通讯作者：
Muchmore, Steven W.
中科院分区：
文献类型：
--
作者：
Brown, Scott P.;Muchmore, Steven W.
我们已经开发了一个系统，用于在企业网格上执行计算，使用一个免费提供的网格计算包，使我们能够从员工桌面计算机上收集未使用的CPU周期。通过修改传统的分子力学公式与泊松-玻尔兹曼表面积（MM-PBSA）的方法，结合一个粗粒度的并行实现适合部署到我们的企业网格，我们表明，它是可能的，以产生快速的基于物理的蛋白质-配体结合亲和力的估计，具有良好的相关性的实验数据。这一点通过检查我们计算的结合亲和力与实验数据的相关性以及与文献中报道的使用传统MM-PBSA计算结合亲和力获得的相关性进行比较来证明。
We have developed a system for performing computations on an enterprise grid using a freely available package for grid computing that allows us to harvest unused CPU cycles off of employee desktop computers. By modifying the traditional formulation of Molecular Mechanics with Poisson-Boltzmann Surface Area (MM-PBSA) methodology, in combination with a coarse-grain parallelized implementation suitable for deployment onto our enterprise grid, we show that it is possible to produce rapid physics-based estimates of protein-ligand binding affinities that have good correlation to experimental data. This is demonstrated by examining the correlation of our calculated binding affinities to experimental data and also by comparison to the correlation obtained from the binding-affinity calculations using traditional MM-PBSA that are reported in the literature.