Socket2: a program for locating, visualizing and analyzing coiled-coil interfaces in protein structures.
Socket2: a program for locating, visualizing and analyzing coiled-coil interfaces in protein structures.
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DOI：
10.1093/bioinformatics/btab631
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发表时间：
2021-12-07
期刊：
影响因子：
--
通讯作者：
Woolfson DN
中科院分区：
文献类型：
--
作者：
Kumar P;Woolfson DN
蛋白质之间的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-螺旋线圈（CC）。因此，在没有专家指导的情况下快速提取、可视化和分析CC接口的能力将促进广泛的生物学研究。在2001年，我们报道了Socket，它基于cc螺旋之间的旋钮入孔（KIH）填充来定位和表征蛋白质结构中的cc。从那时起，对自然和新设计的CCs的研究蓬勃发展，RCSB PDB中的CCs数量迅速增加。因此，我们更新了Socket，使专家和非专业用户都可以访问它。最初的Socket只对最多六个螺旋的cc进行分类。在这里，我们报道了Socket2，它纠正了这种疏忽，以识别具有任意数量螺旋的cc，以及与20个蛋白原残基中的任何一个接口或结合非天然氨基酸的KIH。此外，我们还开发了一个具有附加功能的易于使用的新web服务器。其中包括使用NGL Viewer即时可视化CCs，以及用于查看序列重复、螺旋充填角度和由Socket2识别和计算的CCs的岩心充填几何形状的选项卡。Socket2已在所有现代浏览器上进行了测试。可以在http://coiledcoils.chm.bris.ac.uk/socket2/home.html上免费访问。源代码是使用MIT许可分发的，可以在Socket2主页的Downloads选项卡下下载。
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.
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影响因子：
--
作者：
Lupas AN;Bassler J;Dunin-Horkawicz S
通讯作者：
Dunin-Horkawicz S
影响因子：
5.8
作者：
Rose, Alexander S.;Bradley, Anthony R.;Rose, Peter W.
通讯作者：
Rose, Peter W.
DOI：
10.1002/pro.3279
发表时间：
2018-01
期刊：
Protein science : a publication of the Protein Society
影响因子：
--
作者：
Wood CW;Woolfson DN
通讯作者：
Woolfson DN
影响因子：
5.8
作者：
Guzenko, Dmytro;Strelkov, Sergei V.
通讯作者：
Strelkov, Sergei V.
影响因子：
14.9
作者：
Burley SK;Bhikadiya C;Bi C;Bittrich S;Chen L;Crichlow GV;Christie CH;Dalenberg K;Di Costanzo L;Duarte JM;Dutta S;Feng Z;Ganesan S;Goodsell DS;Ghosh S;Green RK;Guranović V;Guzenko D;Hudson BP;Lawson CL;Liang Y;Lowe R;Namkoong H;Peisach E;Persikova I;Randle C;Rose A;Rose Y;Sali A;Segura J;Sekharan M;Shao C;Tao YP;Voigt M;Westbrook JD;Young JY;Zardecki C;Zhuravleva M
通讯作者：
Zhuravleva M