Ozboyaci Musa, Martinez Michael, Wade Rebecca C
Heidelberg Institute for Theoretical Studies (HITS) , Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany.
Heidelberg Graduate School of Mathematical and Computational Methods for the Sciences, Heidelberg University , INF 205, 69120 Heidelberg, Germany.
J Chem Theory Comput. 2016 Sep 13;12(9):4563-77. doi: 10.1021/acs.jctc.6b00350. Epub 2016 Aug 16.
Computer simulations of molecular systems often make use of regular rectangular grids with equidistant spacing to store information on their molecular interaction fields, e.g., electrostatic potential. These grids provide an easy way to store the data as they do not require any particular specification of the structure of the data. However, such grids may easily become large, and the storage and memory demands may become so high that calculations become infeasible. To overcome this problem, we show here how the data structure DT-Grid can be adapted and applied to efficiently represent macromolecular interaction grids by exploiting the nonuniformity of information on the grid; at the same time, this data structure ensures fast random data access. We demonstrate use of the DT-Grid data structure for potential of mean force and Brownian dynamics simulations of protein-surface binding and macromolecular association with the SDA software. We further demonstrate that the DT-Grid structure enables systems of large size, such as a viral capsid, and high resolution grids to be handled that are beyond current computational feasibility.
分子系统的计算机模拟通常利用具有等间距的规则矩形网格来存储其分子相互作用场的信息，例如静电势。这些网格提供了一种存储数据的简便方法，因为它们不需要对数据结构进行任何特殊指定。然而，这样的网格可能很容易变得很大，存储和内存需求可能变得如此之高，以至于计算变得不可行。为了克服这个问题，我们在此展示如何通过利用网格上信息的不均匀性来调整和应用数据结构DT-Grid，以有效地表示大分子相互作用网格；同时，这种数据结构确保快速随机数据访问。我们展示了使用DT-Grid数据结构进行蛋白质-表面结合以及与SDA软件的大分子缔合的平均力势和布朗动力学模拟。我们进一步证明，DT-Grid结构能够处理当前计算可行性之外的大尺寸系统，例如病毒衣壳，以及高分辨率网格。
