Centre of New Technologies, University of Warsaw, Banacha 2c, Warsaw, Poland.
Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Banacha 2, 02-097 Warsaw, Poland.
Nucleic Acids Res. 2022 Jul 5;50(W1):W44-W50. doi: 10.1093/nar/gkac388.
AlphaKnot is a server that measures entanglement in AlphaFold-solved protein models while considering pLDDT confidence values. AlphaKnot has two main functions: (i) providing researchers with a webserver for analyzing knotting in their own AlphaFold predictions and (ii) providing a database of knotting in AlphaFold predictions from the 21 proteomes for which models have been published prior to 2022. The knotting is defined in a probabilistic fashion. The knotting complexity of proteins is presented in the form of a matrix diagram which shows users the knot type for the entire polypeptide chain and for each of its subchains. The dominant knot types as well as the computed locations of the knot cores (i.e. minimal portions of protein backbones that form a given knot type) are shown for each protein structure. Based mainly on the pLDDT confidence values, entanglements are classified as Knots, Unsure, and Artifacts. The database portion of the server can be used, for example, to examine protein geometry and entanglement-function correlations, as a reference set for protein modeling, and for facilitating evolutional studies. The AlphaKnot server can be found at https://alphaknot.cent.uw.edu.pl/.
AlphaKnot 是一个服务器，用于在考虑 pLDDT 置信值的情况下测量 AlphaFold 解决的蛋白质模型中的纠缠。AlphaKnot 有两个主要功能：（i）为研究人员提供一个用于分析他们自己的 AlphaFold 预测中打结的网络服务器，以及（ii）提供一个包含在 2022 年之前发布模型的 21 个蛋白质组中 AlphaFold 预测中打结的数据库。打结以概率的方式定义。蛋白质的打结复杂性以矩阵图的形式呈现，向用户显示整个多肽链和每个亚链的打结类型。显示每个蛋白质结构的主要打结类型以及计算得出的结核（即形成给定结类型的蛋白质骨架的最小部分）的位置。主要基于 pLDDT 置信值，纠缠被分类为结、不确定和伪影。服务器的数据库部分可用于例如检查蛋白质几何形状和纠缠函数相关性、作为蛋白质建模的参考集以及促进进化研究。AlphaKnot 服务器可以在 https://alphaknot.cent.uw.edu.pl/ 找到。
