Centre of New Technologies, University of Warsaw, Warsaw, Poland.
Faculty of Physics, Astronomy and Applied Computer Science, Jagiellonian University, Cracow, Poland.
Bioinformatics. 2019 Sep 1;35(17):3166-3168. doi: 10.1093/bioinformatics/bty1038.
Links are generalization of knots, that consist of several components. They appear in proteins, peptides and other biopolymers with disulfide bonds or ions interactions giving rise to the exceptional stability. Moreover because of this stability such biopolymers are the target of commercial and medical use (including anti-bacterial and insecticidal activity). Therefore, topological characterization of such biopolymers, not only provides explanation of their thermodynamical or mechanical properties, but paves the way to design templates in pharmaceutical applications. However, distinction between links and trivial topology is not an easy task. Here, we present PyLink-a PyMOL plugin suited to identify three types of links and perform comprehensive topological analysis of proteins rich in disulfide or ion bonds. PyLink can scan for the links automatically, or the user may specify their own components, including closed loops with several bridges and ion interactions. This creates the possibility of designing new biopolymers with desired properties.
The PyLink plugin, manual and tutorial videos are available at http://pylink.cent.uw.edu.pl.
链接是由几个组成部分组成的纽结的推广。它们存在于蛋白质、肽和其他具有二硫键或离子相互作用的生物聚合物中，赋予其异常的稳定性。此外，由于这种稳定性，这些生物聚合物是商业和医疗用途（包括抗菌和杀虫活性）的目标。因此，对这些生物聚合物进行拓扑特征描述不仅可以解释它们的热力学或机械性质，还为药物应用中的模板设计铺平了道路。然而，区分链接和平凡拓扑并不是一件容易的事。在这里，我们介绍了 PyLink，这是一个适合识别三种类型链接并对富含二硫键或离子键的蛋白质进行全面拓扑分析的 PyMOL 插件。PyLink 可以自动扫描链接，或者用户可以指定自己的组件，包括带有多个桥和离子相互作用的闭环。这为设计具有所需性质的新生物聚合物创造了可能性。
PyLink 插件、手册和教程视频可在 http://pylink.cent.uw.edu.pl 获得。
