Applying graph theory to protein structures: an Atlas of coiled coils.
Applying graph theory to protein structures: an Atlas of coiled coils.
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DOI：
10.1093/bioinformatics/bty347
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发表时间：
2018-10-01
期刊：
影响因子：
--
通讯作者：
Woolfson DN
中科院分区：
文献类型：
--
作者：
Heal JW;Bartlett GJ;Wood CW;Thomson AR;Woolfson DN
为了充分理解蛋白质的结构、折叠和功能，并可靠地从头设计蛋白质，我们必须从实验表征的天然蛋白质结构中学习。可用的蛋白质结构数量很大，并且呈指数级增长，这使得这项任务具有挑战性。事实上，计算资源对于分类和分析这种资源变得越来越重要。在这里，我们使用图论的工具来定义一个Atlas分类方案，用于自动分类某些蛋白质子结构。针对蛋白质-结构和蛋白质-蛋白质相互作用基序中普遍存在的α-螺旋卷曲螺旋，我们提出了一套用于分析这些组装体的计算资源。iSOCKET能够对蛋白质内的侧链包装进行交互式分析，以自动识别卷曲螺旋，并具有相当大的用户控制。将基于图论的Atlas分类方案应用于iSOCKET识别的结构，给出了螺旋弹簧圈图谱，这是对现存螺旋弹簧圈的全自动更新概述。这种方法的实用性说明了第一次正式分类的一个新兴的子类的线圈线圈称为α-螺旋桶。此外，在图集中，已知的卷曲螺旋宇宙与卷曲螺旋结构的“暗物质”的部分枚举一起呈现;即那些理论上可能但迄今尚未观察到的卷曲螺旋结构，因此为蛋白质设计提供了定义的目标。iSOCKET作为与此工作相关的开源GitHub存储库的一部分提供（https：//github.com/woolfson-group/isocket）。该存储库还包含对蛋白质图进行分类时生成的所有数据。可在http://coiledcoils.chm.bris.ac.uk/atlas/app上获得线圈图集。
To understand protein structure, folding and function fully and to design proteins de novo reliably, we must learn from natural protein structures that have been characterized experimentally. The number of protein structures available is large and growing exponentially, which makes this task challenging. Indeed, computational resources are becoming increasingly important for classifying and analyzing this resource. Here, we use tools from graph theory to define an Atlas classification scheme for automatically categorizing certain protein substructures. Focusing on the α-helical coiled coils, which are ubiquitous protein-structure and protein–protein interaction motifs, we present a suite of computational resources designed for analyzing these assemblies. iSOCKET enables interactive analysis of side-chain packing within proteins to identify coiled coils automatically and with considerable user control. Applying a graph theory-based Atlas classification scheme to structures identified by iSOCKET gives the Atlas of Coiled Coils, a fully automated, updated overview of extant coiled coils. The utility of this approach is illustrated with the first formal classification of an emerging subclass of coiled coils called α-helical barrels. Furthermore, in the Atlas, the known coiled-coil universe is presented alongside a partial enumeration of the ‘dark matter’ of coiled-coil structures; i.e. those coiled-coil architectures that are theoretically possible but have not been observed to date, and thus present defined targets for protein design. iSOCKET is available as part of the open-source GitHub repository associated with this work (https://github.com/woolfson-group/isocket). This repository also contains all the data generated when classifying the protein graphs. The Atlas of Coiled Coils is available at: http://coiledcoils.chm.bris.ac.uk/atlas/app.
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影响因子：
5.6
作者：
Grigoryan G;Degrado WF
通讯作者：
Degrado WF
影响因子：
64.8
作者：
Grigoryan, Gevorg;Reinke, Aaron W.;Keating, Amy E.
通讯作者：
Keating, Amy E.
DOI：
10.1126/science.1261172
发表时间：
2014-12-19
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Joh NH;Wang T;Bhate MP;Acharya R;Wu Y;Grabe M;Hong M;Grigoryan G;DeGrado WF
通讯作者：
DeGrado WF
影响因子：
2.9
作者：
Fraga, Keith J.;Joo, Hyun;Tsai, Jerry
通讯作者：
Tsai, Jerry
DOI：
10.1073/pnas.0604871103
发表时间：
2006-10-17
影响因子：
11.1
作者：
Liu, Jie;Zheng, Qi;Lu, Min
通讯作者：
Lu, Min