Surveying Molecular Interactions with DOT

L. T. Eyck, J. Mandell, V. Roberts, M. Pique
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引用次数: 61

Abstract

The purpose of the molecular interaction program DOT (Daughter of Turnip) is rapid computation of the electrostatic potential energy between two proteins or other charged molecules. DOT exhaustively tests all six degrees of freedom, rotational and translational, and produces a grid of approximate interaction energies and orientations. It is able to do this because the problem is cast as the convolution of the potential field of the first molecule and any rotated charge distribution of the second. The algorithm lends itself to both parallelization and vectorization, permitting huge increases in computational speed over other methods for obtaining the same information. For example, a complete mapping of interactions between plastocyanin and cytochrome c was done in eight minutes using 256 nodes of an Intel Paragon. DOT is expected to be particularly useful as a rapid screen to find configurations for more detailed study using exact energy models.
用DOT测量分子相互作用
分子相互作用程序DOT(萝卜之子)的目的是快速计算两个蛋白质或其他带电分子之间的静电势能。DOT详尽地测试了所有六个自由度,旋转和平移,并产生了一个近似的相互作用能量和方向的网格。之所以能够这样做,是因为这个问题是第一个分子的势场和第二个分子的任意旋转电荷分布的卷积。该算法同时适用于并行化和向量化,与获取相同信息的其他方法相比,可以大大提高计算速度。例如,使用Intel Paragon的256个节点,在8分钟内完成了质体青素和细胞色素c之间相互作用的完整映射。DOT被认为是一种特别有用的快速筛选方法,可以使用精确的能量模型找到更详细的研究配置。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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