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Discrete Molecular Dynamics Approach to the Study of Disordered and Aggregating Proteins

机译:离散分子动力学方法研究无序聚集蛋白

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摘要

We present a refinement of the Coarse Grained PACSAB force field for Discrete Molecular Dynamics (DMD) simulations of proteins in aqueous conditions. As the original version, the refined method provides good representation of the structure and dynamics of folded proteins but provides much better representations of a variety of unfolded proteins, including some very large, impossible to analyze by atomistic simulation methods. The PACSAB/DMD method also reproduces accurately aggregation properties, providing good pictures of the structural ensembles of proteins showing a folded core and an intrinsically disordered region. The combination of accuracy and speed makes the method presented here a good alternative for the exploration of unstructured protein systems.
机译:我们提出了粗粒PACSAB力场的改进,用于蛋白质在水性条件下的离散分子动力学(DMD)模拟。作为原始版本,改进的方法可以很好地表示折叠蛋白质的结构和动力学,但可以更好地表示各种未折叠蛋白质,包括一些非常大的,无法通过原子模拟方法进行分析的蛋白质。 PACSAB / DMD方法还可以准确地重现聚集特性,从而提供蛋白质结构整体的良好图像,显示折叠的核心和固有的无序区域。准确性和速度的结合使此处介绍的方法成为探索非结构化蛋白质系统的理想选择。

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