School of Chemistry, University of Bristol, Bristol BS8 1TS, UK.
School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK.
Bioinformatics. 2021 Dec 7;37(23):4575-4577. doi: 10.1093/bioinformatics/btab631.
Protein-protein interactions are central to all biological processes. One frequently observed mode of such interactions is the α-helical coiled coil (CC). Thus, an ability to extract, visualize and analyze CC interfaces quickly and without expert guidance would facilitate a wide range of biological research. In 2001, we reported Socket, which locates and characterizes CCs in protein structures based on the knobs-into-holes (KIH) packing between helices in CCs. Since then, studies of natural and de novo designed CCs have boomed, and the number of CCs in the RCSB PDB has increased rapidly. Therefore, we have updated Socket and made it accessible to expert and nonexpert users alike.
The original Socket only classified CCs with up to six helices. Here, we report Socket2, which rectifies this oversight to identify CCs with any number of helices, and KIH interfaces with any of the 20 proteinogenic residues or incorporating nonnatural amino acids. In addition, we have developed a new and easy-to-use web server with additional features. These include the use of NGL Viewer for instantly visualizing CCs, and tabs for viewing the sequence repeats, helix-packing angles and core-packing geometries of CCs identified and calculated by Socket2.
Socket2 has been tested on all modern browsers. It can be accessed freely at http://coiledcoils.chm.bris.ac.uk/socket2/home.html. The source code is distributed using an MIT licence and available to download under the Downloads tab of the Socket2 home page.
蛋白质-蛋白质相互作用是所有生物过程的核心。这种相互作用的一种常见模式是α-螺旋卷曲螺旋（CC）。因此，能够快速、无需专家指导地提取、可视化和分析 CC 界面，将极大地促进广泛的生物学研究。2001 年，我们报告了 Socket，它基于 CC 中螺旋之间的旋钮入孔（KIH）包装，定位和描述蛋白质结构中的 CC。自那时以来，天然和从头设计的 CC 的研究蓬勃发展，RCSB PDB 中的 CC 数量迅速增加。因此，我们更新了 Socket，并使专家和非专家用户都可以使用它。
原始的 Socket 只能分类多达六个螺旋的 CC。在这里，我们报告了 Socket2，它纠正了这一疏忽，以识别具有任意数量的螺旋和 KIH 接口的 CC，以及 20 种蛋白质残基中的任意一种或包含非天然氨基酸。此外，我们开发了一个新的、易于使用的带有附加功能的网络服务器。这些功能包括使用 NGL Viewer 即时可视化 CC，以及用于查看由 Socket2 识别和计算的 CC 的序列重复、螺旋包装角度和核心包装几何形状的选项卡。
Socket2 已在所有现代浏览器上进行了测试。它可以免费访问 http://coiledcoils.chm.bris.ac.uk/socket2/home.html。源代码使用 MIT 许可证分发，并可在 Socket2 主页的“下载”选项卡中下载。
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