Matching Multiple Rigid Domain Decompositions of Proteins.
Matching Multiple Rigid Domain Decompositions of Proteins.
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DOI：
10.1109/tnb.2017.2660538
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发表时间：
2017-03
影响因子：
3.9
通讯作者：
Streinu I
中科院分区：
文献类型：
--
作者：
Flynn E;Streinu I
我们描述了有效的方法，一致的着色和可视化的刚性集群分解从蛋白质结构的变化获得的集合，并奠定了基础，更复杂的设置，可能涉及不同的计算和实验方法。这里的重点是三个生物学应用：概念上更简单的问题，可视化稀释和突变分析的结果，以及更复杂的任务，匹配同一蛋白质的多个NMR模型的分解。在KINARI Web服务器应用程序中实现，改进的可视化技术提供了有关蛋白质折叠核心的有用信息，有助于检查突变对蛋白质灵活性和功能的影响，并提供了对PDB蛋白质结构运动的见解。开发这些工具的目的是改进和验证刚性分析，作为一种可靠的粗粒度模型，捕获有关蛋白质在天然状态附近缓慢运动的基本信息。
We describe efficient methods for consistently coloring and visualizing collections of rigid cluster decompositions obtained from variations of a protein structure, and lay the foundation for more complex setups that may involve different computational and experimental methods. The focus here is on three biological applications: the conceptually simpler problems of visualizing results of dilution and mutation analyses, and the more complex task of matching decompositions of multiple NMR models of the same protein. Implemented into the KINARI web server application, the improved visualization techniques give useful information about protein folding cores, help examining the effect of mutations on protein flexibility and function, and provide insights into the structural motions of PDB proteins solved with solution NMR. These tools have been developed with the goal of improving and validating rigidity analysis as a credible coarse-grained model capturing essential information about a protein’s slow motions near the native state.