Goundaroulis Dimos, Gügümcü Neslihan, Lambropoulou Sofia, Dorier Julien, Stasiak Andrzej, Kauffman Louis
Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland.
SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.
Polymers (Basel). 2017 Sep 13;9(9):444. doi: 10.3390/polym9090444.
In this paper we introduce a method that offers a detailed overview of the entanglement of an open protein chain. Further, we present a purely topological model for classifying open protein chains by also taking into account any bridge involving the backbone. To this end, we implemented the concepts of planar knotoids and bonded knotoids. We show that the planar knotoids technique provides more refined information regarding the knottedness of a protein when compared to established methods in the literature. Moreover, we demonstrate that our topological model for bonded proteins is robust enough to distinguish all types of lassos in proteins.
在本文中，我们介绍了一种方法，该方法能详细概述开放蛋白质链的缠结情况。此外，我们还提出了一个纯拓扑模型，通过考虑涉及主链的任何桥接结构来对开放蛋白质链进行分类。为此，我们实现了平面纽结体和键合纽结体的概念。我们表明，与文献中的现有方法相比，平面纽结体技术能提供有关蛋白质打结情况的更精确信息。此外，我们证明了我们的键合蛋白质拓扑模型足够稳健，能够区分蛋白质中所有类型的套索结构。
