TopoLink: evaluation of structural models using chemical crosslinking distance constraints
TopoLink: evaluation of structural models using chemical crosslinking distance constraints
复制标题
DOI：
10.1093/bioinformatics/btz014
复制
发表时间：
2019-09-01
期刊：
影响因子：
5.8
通讯作者：
Martinez, Leandro
中科院分区：
文献类型：
--
作者：
Ferrari, Allan J. R.;Clasen, Milan A.;Martinez, Leandro
摘要：开发了一个利用化学交联实验评价结构模型的软件。用户提供所使用的连接物的类型及其反应性，以及观察到的交联物和死胡同。该软件计算连接感兴趣的活性原子的物理启发连接体的最小长度，并报告每个距离与实验观察的一致性。提供了模型与链接一致性的统计数据。开发了评估模型集合中交联链相关性的工具。使用TopLink评估CATH数据库所有结构的潜在交联链。作为蛋白质大小和连接物长度的函数的交联物的数目可用于指导实验设计。
The Summary: A software was developed to evaluate structural models using chemical crosslinking experiments. The user provides the types of linkers used and their reactivity, and the observed crosslinks and dead-ends. The software computes the minimum length of a physically inspired linker that connects the reactive atoms of interest, and reports the consistency of each distance with the experimental observation. Statistics on model consistency with the links are provided. Tools to evaluate the correlation of crosslinks in ensembles of models were developed. TopoLink was used to evaluate the potential crosslinks of all structures of the CATH database. The number of crosslinks expected as a function of protein size and linker length can be used as guide for experimental design.