JASSA: a comprehensive tool for prediction of SUMOylation sites and SIMs
JASSA: a comprehensive tool for prediction of SUMOylation sites and SIMs
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DOI：
10.1093/bioinformatics/btv403
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发表时间：
2015-11-01
期刊：
影响因子：
5.8
通讯作者：
Zamborlini, Alessia
中科院分区：
文献类型：
--
作者：
Beauclair, Guillaume;Bridier-Nahmias, Antoine;Zamborlini, Alessia
动机：小泛素样修饰蛋白（SUMO）的翻译后修饰（SUMO化）参与了许多基本的细胞过程。SUMO蛋白与蛋白质底物结合，产生一个界面，用于招募含有SUMO相互作用基序（西姆斯）的辅因子。定位SUMO结合位点和西姆斯是研究SUMO化的功能结果所必需的。为了确定实验验证的最佳候选位点，我们设计了JASSA，SUMOylation位点和西姆斯.Results的联合分析仪：JASSA是一个预测器，它使用基于位置频率矩阵的评分系统，该矩阵来自实验SUMOylation位点或西姆斯的比对。与现有的Web工具相比，JASSA表现出相当或更好的性能。实现了新的功能，以更好地评估预测，包括识别匹配查询序列的数据库命中和二级结构元件内的候选位点的表示和/或感兴趣的蛋白质的3D折叠，可从存放的PDB文件中检索。
Motivation: Post-translational modification by the Small Ubiquitin-like Modifier (SUMO) proteins, a process termed SUMOylation, is involved in many fundamental cellular processes. SUMO proteins are conjugated to a protein substrate, creating an interface for the recruitment of cofactors harboring SUMO-interacting motifs (SIMs). Mapping both SUMO-conjugation sites and SIMs is required to study the functional consequence of SUMOylation. To define the best candidate sites for experimental validation we designed JASSA, a Joint Analyzer of SUMOylation site and SIMs.Results: JASSA is a predictor that uses a scoring system based on a Position Frequency Matrix derived from the alignment of experimental SUMOylation sites or SIMs. Compared with existing web-tools, JASSA displays on par or better performances. Novel features were implemented towards a better evaluation of the prediction, including identification of database hits matching the query sequence and representation of candidate sites within the secondary structural elements and/or the 3D fold of the protein of interest, retrievable from deposited PDB files.