dbPTM 2016: 10-year anniversary of a resource for post-translational modification of proteins.
dbPTM 2016: 10-year anniversary of a resource for post-translational modification of proteins.
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DOI：
10.1093/nar/gkv1240
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发表时间：
2016-01-04
影响因子：
14.9
通讯作者：
Lee TY
中科院分区：
文献类型：
--
作者：
Huang KY;Su MG;Kao HJ;Hsieh YC;Jhong JH;Cheng KH;Huang HD;Lee TY
由于蛋白质的翻译后修饰（PTMs）在调节生物过程中的重要性，dbPTM （http://dbPTM.mbc.nctu.edu.tw/）被开发为一个综合数据库，从几个数据库中经过实验验证的PTMs，并注释了所有UniProtKB蛋白质条目的潜在PTMs。在dbPTM成立10周年之际，更新的资源不仅提供了实验验证的PTM的综合数据集，而且还提供了一个集成接口，用于访问与PTM分析相关的所有可用数据库和工具。除了从14个公共数据库中收集实验PTM数据外，本次更新还通过文本挖掘从大约500篇研究文章中手动整理了超过12000个修饰肽，包括新兴的s -亚硝基化、s -谷胱甘肽化和琥珀酰化。随着可用的PTM预测方法数量的增加，本工作编制了一个非同源基准数据集来评估在线PTM预测工具的预测能力。对PTM底物位点结构研究的兴趣日益浓厚，促使所有实验PTM肽基于数据库标识符和序列识别将其映射到蛋白质数据库（PDB）的蛋白质条目，这使得用户能够检查空间邻近的氨基酸，溶剂可及的表面积和PTM底物位点在三级结构上的侧链取向。由于PDB中的药物结合有注释，本次更新确定了超过1100个与药物结合相关的PTM位点。该更新还集成了代谢途径和蛋白质-蛋白质相互作用，以支持一组蛋白质的PTM网络分析。最后，对web界面进行了重新设计和增强，以方便对该资源的访问。
Owing to the importance of the post-translational modifications (PTMs) of proteins in regulating biological processes, the dbPTM (http://dbPTM.mbc.nctu.edu.tw/) was developed as a comprehensive database of experimentally verified PTMs from several databases with annotations of potential PTMs for all UniProtKB protein entries. For this 10th anniversary of dbPTM, the updated resource provides not only a comprehensive dataset of experimentally verified PTMs, supported by the literature, but also an integrative interface for accessing all available databases and tools that are associated with PTM analysis. As well as collecting experimental PTM data from 14 public databases, this update manually curates over 12 000 modified peptides, including the emerging S-nitrosylation, S-glutathionylation and succinylation, from approximately 500 research articles, which were retrieved by text mining. As the number of available PTM prediction methods increases, this work compiles a non-homologous benchmark dataset to evaluate the predictive power of online PTM prediction tools. An increasing interest in the structural investigation of PTM substrate sites motivated the mapping of all experimental PTM peptides to protein entries of Protein Data Bank (PDB) based on database identifier and sequence identity, which enables users to examine spatially neighboring amino acids, solvent-accessible surface area and side-chain orientations for PTM substrate sites on tertiary structures. Since drug binding in PDB is annotated, this update identified over 1100 PTM sites that are associated with drug binding. The update also integrates metabolic pathways and protein–protein interactions to support the PTM network analysis for a group of proteins. Finally, the web interface is redesigned and enhanced to facilitate access to this resource.