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生物分子相互作用的粗粒度(混合)整合建模

Coarse-grained (hybrid) integrative modeling of biomolecular interactions.

作者信息

Roel-Touris Jorge, Bonvin Alexandre M J J

机构信息

Bijvoet Centre for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Utrecht 3584CH, the Netherlands.

出版信息

Comput Struct Biotechnol J. 2020 May 15;18:1182-1190. doi: 10.1016/j.csbj.2020.05.002. eCollection 2020.

Abstract

The computational modeling field has vastly evolved over the past decades. The early developments of simplified protein systems represented a stepping stone towards establishing more efficient approaches to sample intricated conformational landscapes. Downscaling the level of resolution of biomolecules to coarser representations allows for studying protein structure, dynamics and interactions that are not accessible by classical atomistic approaches. The combination of different resolutions, namely hybrid modeling, has also been proved as an alternative when mixed levels of details are required. In this review, we provide an overview of coarse-grained/hybrid models focusing on their applicability in the modeling of biomolecular interactions. We give a detailed list of ready-to-use modeling software for studying biomolecular interactions allowing various levels of coarse-graining and provide examples of complexes determined by integrative coarse-grained/hybrid approaches in combination with experimental information.

摘要

在过去几十年中,计算建模领域有了巨大的发展。早期简化蛋白质系统的发展是迈向建立更有效方法以采样复杂构象景观的垫脚石。将生物分子的分辨率水平降低到更粗糙的表示形式,使得研究经典原子方法无法触及的蛋白质结构、动力学和相互作用成为可能。当需要混合细节水平时,不同分辨率的组合,即混合建模,也被证明是一种替代方法。在本综述中,我们概述了粗粒度/混合模型,重点介绍它们在生物分子相互作用建模中的适用性。我们给出了一份用于研究生物分子相互作用的现成建模软件的详细列表,这些软件允许不同程度的粗粒度,并提供了结合实验信息通过综合粗粒度/混合方法确定的复合物实例。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6cea/7264466/e618fe179252/ga1.jpg

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