Visualizing Motional Correlations in Molecular Dynamics using Geometric Deformations
Visualizing Motional Correlations in Molecular Dynamics using Geometric Deformations
复制标题
使用几何变形可视化分子动力学中的运动相关性
DOI：
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发表时间：
2013
期刊：
影响因子：
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通讯作者：
P. Rheingans
中科院分区：
文献类型：
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作者：
Matthew Fioravante;Adam Shook;Ian F. Thorpe;P. Rheingans
在大分子中，当分子的一个位点的变化影响到远处的位点时，就会发生变构效应。理解这些变构效应对于理解复杂分子（如蛋白质）的功能是如何被调节的很重要。这种知识的一个潜在应用是开发小分子，改变与疾病有关的蛋白质的功能。研究运动相关性可以帮助研究人员发现源位点的变化如何影响靶位点，从而发现可作为药物的变构配体如何发挥其治疗作用。通过提高我们分析这些相关关系的能力，我们有可能开发出新的药物来对抗致命的疾病，如丙型肝炎。我们提出了四种视觉技术，在渲染的三维分子模型上表示情感相关性，提供了观察相关残基簇和变构相互作用路径的新方法。这些技术给我们提供了一种研究复杂分子中存在的运动相关性的新方法。我们比较了每一种技术，以确定哪种技术对表示情感相关性最有用。
In macromolecules, an allosteric effect is said to occur when a change at one site of a molecule affects a distant site. Understanding these allosteric effects can be important for understanding how the functions of complex molecules such as proteins are regulated. One potential application of this knowledge is the development of small molecules that alter the function of proteins involved in diseases. Studying motional correlation can help researchers to discover how a change at a source site affects the target site and thus how allosteric ligands that could serve as drugs are able to exert their therapeutic effects. By improving our ability to analyze these correlated relationships, it may be possible to develop new medications to combat deadly diseases such as Hepatitis C. We present four visual techniques which represent motional correlation on rendered three‐dimensional molecular models, providing new ways to view clusters of correlated residues and paths of allosteric interactions. These techniques give us a new way of investigating the presence of motional correlations in complex molecules. We compare each of these techniques to determine which are the most useful for representing motional correlations.
影响因子：
5.5
作者：
VanWart, Adam T.;Eargle, John;Luthey-Schulten, Zaida;Amaro, Rommie E.
通讯作者：
Amaro, Rommie E.