XLinkDB 2.0: integrated, large-scale structural analysis of protein crosslinking data
XLinkDB 2.0: integrated, large-scale structural analysis of protein crosslinking data
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DOI：
10.1093/bioinformatics/btw232
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发表时间：
2016-09-01
期刊：
影响因子：
5.8
通讯作者：
Bruce, James E.
中科院分区：
文献类型：
--
作者：
Schweppe, Devin K.;Zheng, Chunxiang;Bruce, James E.
动机：大规模化学交联质谱（XL-MS）分析正迅速成为高通量测定蛋白质结构信息和蛋白质-蛋白质相互作用的有力手段。最近的研究已经收集了数千个交联的相互作用，但该领域缺乏有效的工具来编译实验数据或访问这些大规模分析的网络和结构知识。我们提出了XLinkDB 2.0，它集成了网络分析，蛋白质数据库查询，预测蛋白质结构建模和对接蛋白质结构建模的工具。XLinkDB 2.0的新的集成方法使XL-MS蛋白质相互作用数据的整体分析成为可能，而不限于用于分析的交联剂或分析系统。
Motivation: Large-scale chemical cross-linking with mass spectrometry (XL-MS) analyses are quickly becoming a powerful means for high-throughput determination of protein structural information and protein-protein interactions. Recent studies have garnered thousands of cross-linked interactions, yet the field lacks an effective tool to compile experimental data or access the network and structural knowledge for these large scale analyses. We present XLinkDB 2.0 which integrates tools for network analysis, Protein Databank queries, modeling of predicted protein structures and modeling of docked protein structures. The novel, integrated approach of XLinkDB 2.0 enables the holistic analysis of XL-MS protein interaction data without limitation to the cross-linker or analytical system used for the analysis.