GRPY：一种用于计算刚性生物大分子流体力学性质的精确珠粒方法。
GRPY: An Accurate Bead Method for Calculation of Hydrodynamic Properties of Rigid Biomacromolecules.
机构信息
Department of Biosystems and Soft Matter, Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw, Poland; Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, New Jersey.
Institute of Theoretical Physics, Faculty of Physics, University of Warsaw, Warsaw, Poland.
出版信息
Biophys J. 2018 Sep 4;115(5):782-800. doi: 10.1016/j.bpj.2018.07.015. Epub 2018 Jul 24.
Abstract
Two main problems that arise in the context of hydrodynamic bead modeling are an inaccurate treatment of bead overlaps and the necessity of using volume corrections when calculating intrinsic viscosity. We present a formalism based on the generalized Rotne-Prager-Yamakawa approximation that successfully addresses both of these issues. The generalized Rotne-Prager-Yamakawa method is shown to be highly effective for the calculation of transport properties of rigid biomolecules represented as assemblies of spherical beads of different sizes, both overlapping and nonoverlapping. We test the method on simple molecular shapes as well as real protein structures and compare its performance with other computational approaches.
摘要
在流体动力珠粒建模的背景下，出现了两个主要问题，即珠粒重叠的处理不准确和计算特性粘度时需要使用体积修正。我们提出了一种基于广义 Rotne-Prager-Yamakawa 逼近的形式主义，成功地解决了这两个问题。事实证明，广义 Rotne-Prager-Yamakawa 方法对于计算由不同大小的球形珠粒组装而成的刚性生物分子的输运性质非常有效，无论是重叠的还是不重叠的珠粒。我们在简单的分子形状以及真实的蛋白质结构上测试了该方法，并将其性能与其他计算方法进行了比较。
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