DbPTM 3.0: an informative resource for investigating substrate site specificity and functional association of protein post-translational modifications.
DbPTM 3.0: an informative resource for investigating substrate site specificity and functional association of protein post-translational modifications.
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DBPTM 3.0：研究蛋白质后翻译后修饰的基材位点特异性和功能关联的信息资源。
DOI：
10.1093/nar/gks1229
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发表时间：
2013-01
影响因子：
14.9
通讯作者：
Huang HD
中科院分区：
文献类型：
--
作者：
Lu CT;Huang KY;Su MG;Lee TY;Bretaña NA;Chang WC;Chen YJ;Chen YJ;Huang HD
蛋白质修饰是一种极其重要的翻译后调节，它调节蛋白质的理化性质、构象、稳定性和活性，从而改变蛋白质的功能。由于基于质谱（MS）的方法在鉴定位点特异性翻译后修饰（PTM）方面的高通量，更新了dbPTM（http：//dbPTM.mbc.nctu.edu.tw/），以整合从公共资源获得的实验PTM以及与来自研究文章的PTM相关的手动管理的MS/MS肽。dbPTM的3.0版旨在成为一个信息资源，用于研究PTM位点的底物特异性和底物与其相互作用蛋白之间PTM的功能关联。为了研究修饰位点的底物特异性，一种新开发的统计方法已被应用于确定每种类型的PTM包含足够的实验数据的显着的底物基序。根据dbPTM中的数据统计，>60%的PTM位点位于蛋白质的功能结构域中。众所周知，大多数PTM可以为特定的蛋白质相互作用结构域创建结合位点，这些蛋白质相互作用结构域一起工作以实现细胞功能。因此，该更新整合了蛋白质-蛋白质相互作用和结构域-结构域相互作用，以确定位于蛋白质相互作用结构域中的PTM位点的功能关联。此外，跨膜（TM）蛋白的结构拓扑信息集成在dbPTM中，以描绘报告的PTM网站和TM拓扑结构之间的结构相关性。为了便于研究TM蛋白上的PTM，PTM底物位点和结构拓扑以图形方式表示。此外，文献信息相关的PTM，orthopathic保护和基板图案的PTM也提供了资源。最后，该版本具有改进的Web界面，以方便访问资源。
Protein modification is an extremely important post-translational regulation that adjusts the physical and chemical properties, conformation, stability and activity of a protein; thus altering protein function. Due to the high throughput of mass spectrometry (MS)-based methods in identifying site-specific post-translational modifications (PTMs), dbPTM (http://dbPTM.mbc.nctu.edu.tw/) is updated to integrate experimental PTMs obtained from public resources as well as manually curated MS/MS peptides associated with PTMs from research articles. Version 3.0 of dbPTM aims to be an informative resource for investigating the substrate specificity of PTM sites and functional association of PTMs between substrates and their interacting proteins. In order to investigate the substrate specificity for modification sites, a newly developed statistical method has been applied to identify the significant substrate motifs for each type of PTMs containing sufficient experimental data. According to the data statistics in dbPTM, >60% of PTM sites are located in the functional domains of proteins. It is known that most PTMs can create binding sites for specific protein-interaction domains that work together for cellular function. Thus, this update integrates protein–protein interaction and domain–domain interaction to determine the functional association of PTM sites located in protein-interacting domains. Additionally, the information of structural topologies on transmembrane (TM) proteins is integrated in dbPTM in order to delineate the structural correlation between the reported PTM sites and TM topologies. To facilitate the investigation of PTMs on TM proteins, the PTM substrate sites and the structural topology are graphically represented. Also, literature information related to PTMs, orthologous conservations and substrate motifs of PTMs are also provided in the resource. Finally, this version features an improved web interface to facilitate convenient access to the resource.
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基因本体论：2011年的增强。
影响因子：
14.9
作者：
Gene Ontology Consortium
通讯作者：
Gene Ontology Consortium
影响因子：
4.4
作者：
Chen, Yi-Ju;Ku, Wei-Chi;Chen, Yu-Ju
通讯作者：
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影响因子：
14.9
作者：
BAIROCH, A
通讯作者：
BAIROCH, A
影响因子：
14.9
作者：
Dinkel H;Chica C;Via A;Gould CM;Jensen LJ;Gibson TJ;Diella F
通讯作者：
Diella F
影响因子：
14.9
作者：
Chatr-aryamontri, Andrew;Ceol, Arnaud;Palazzi, Luisa Montecchi;Nardelli, Giuliano;Schneider, Maria Victoria;Castagnoli, Luisa;Cesareni, Gianni
通讯作者：
Cesareni, Gianni