Dabrowski-Tumanski Pawel, Jarmolinska Aleksandra I, Niemyska Wanda, Rawdon Eric J, Millett Kenneth C, Sulkowska Joanna I
Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093, Warsaw, Poland.
Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland.
Nucleic Acids Res. 2017 Jan 4;45(D1):D243-D249. doi: 10.1093/nar/gkw976. Epub 2016 Oct 28.
Protein chains are known to fold into topologically complex shapes, such as knots, slipknots or complex lassos. This complex topology of the chain can be considered as an additional feature of a protein, separate from secondary and tertiary structures. Moreover, the complex topology can be defined also as one additional structural level. The LinkProt database (http://linkprot.cent.uw.edu.pl) collects and displays information about protein links - topologically non-trivial structures made by up to four chains and complexes of chains (e.g. in capsids). The database presents deterministic links (with loops closed, e.g. by two disulfide bonds), links formed probabilistically and macromolecular links. The structures are classified according to their topology and presented using the minimal surface area method. The database is also equipped with basic tools which allow users to analyze the topology of arbitrary (bio)polymers.
已知蛋白质链会折叠成拓扑结构复杂的形状，如纽结、活结或复杂的套索。链的这种复杂拓扑结构可被视为蛋白质的一个附加特征，与二级和三级结构不同。此外，复杂拓扑结构也可被定义为一个附加的结构层次。LinkProt数据库（http://linkprot.cent.uw.edu.pl）收集并展示有关蛋白质链接的信息——由多达四条链及链复合物（如衣壳中的）构成的拓扑非平凡结构。该数据库呈现确定性链接（环闭合，如通过两个二硫键）、概率性形成的链接以及大分子链接。这些结构根据其拓扑结构进行分类，并使用最小表面积法展示。该数据库还配备了基本工具，允许用户分析任意（生物）聚合物的拓扑结构。
