The shadow map: a general contact definition for capturing the dynamics of biomolecular folding and function.
The shadow map: a general contact definition for capturing the dynamics of biomolecular folding and function.
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DOI：
10.1021/jp300852d
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发表时间：
2012-07-26
影响因子：
3.3
通讯作者：
Onuchic, Jose N.
中科院分区：
文献类型：
--
作者：
Noel, Jeffrey K.;Whitford, Paul C.;Onuchic, Jose N.
基于结构的模型（SBM）是从漏斗能量景观中产生的生物分子动力学的简化模型。我们最近介绍了一种全原子SBM，它明确表示生物分子的原子几何形状。虽然这项初步研究表明，所有原子的SBM哈密顿量的鲁棒性的变化，在许多充满活力的参数，一个重要的方面，这还没有被探索过，是本机相互作用的定义。在这项研究中，我们提出了一个通用的定义，用于生成原子粒度的接触映射称为“阴影”。阴影算法最初考虑截止距离内的所有原子，然后由筛选参数控制，丢弃被遮挡的接触。我们表明，这种选择的接触地图不仅表现良好的蛋白质折叠，因为它产生一致的合作折叠行为的SBMs，但也希望探索动态的大分子组装，因为它分配能量类似的RNA和蛋白质之间，尽管他们不同的内部包装。基于全原子结构的模型采用阴影接触映射，为探索生物分子的几何特征，特别是折叠和功能之间的联系提供了一个通用的框架。
Structure-based models (SBMs) are simplified models of the biomolecular dynamics that arise from funneled energy landscapes. We recently introduced an all-atom SBM that explicitly represents the atomic geometry of a biomolecule. While this initial study showed the robustness of the all-atom SBM Hamiltonian to changes in many of the energetic parameters, an important aspect, which has not been explored previously, is the definition of native interactions. In this study, we propose a general definition for generating atomically-grained contact maps called “Shadow.” The Shadow algorithm initially considers all atoms within a cutoff distance and then, controlled by a screening parameter, discards the occluded contacts. We show that this choice of contact map is not only well behaved for protein folding, since it produces consistently cooperative folding behavior in SBMs, but also desirable for exploring the dynamics of macromolecular assemblies since it distributes energy similarly between RNAs and proteins despite their disparate internal packing. All-atom structure-based models employing Shadow contact maps provide a general framework for exploring the geometrical features of biomolecules, especially the connections between folding and function.
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影响因子：
5.5
作者：
Hess, Berk;Kutzner, Carsten;Lindahl, Erik
通讯作者：
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影响因子：
4.4
作者：
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作者：
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DOI：
10.1073/pnas.2534828100
发表时间：
2004-01-13
影响因子：
11.1
作者：
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通讯作者：
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影响因子：
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作者：
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