Standley Daron M, Kinjo Akira R, Kinoshita Kengo, Nakamura Haruki
Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan.
Brief Bioinform. 2008 Jul;9(4):276-85. doi: 10.1093/bib/bbn015. Epub 2008 Apr 22.
The Protein Data Bank Japan (PDBj) curates, edits and distributes protein structural data as a member of the worldwide Protein Data Bank (wwPDB) and currently processes approximately 25-30% of all deposited data in the world. Structural information is enhanced by the addition of biological and biochemical functional data as well as experimental details extracted from the literature and other databases. Several applications have been developed at PDBj for structural biology and biomedical studies: (i) a Java-based molecular graphics viewer, jV; (ii) display of electron density maps for the evaluation of structure quality; (iii) an extensive database of molecular surfaces for functional sites, eF-site, as well as a search service for similar molecular surfaces, eF-seek; (iv) identification of sequence and structural neighbors; (v) a graphical user interface to all known protein folds with links to the above applications, Protein Globe. Recent examples are shown that highlight the utility of these tools in recognizing remote homologies between pairs of protein structures and in assigning putative biochemical functions to newly determined targets from structural genomics projects.
日本蛋白质数据库（PDBj）作为全球蛋白质数据库（wwPDB）的成员，负责整理、编辑和分发蛋白质结构数据，目前处理全球约25%-30%的所有存入数据。通过添加生物和生化功能数据以及从文献和其他数据库中提取的实验细节，结构信息得到了增强。PDBj已经开发了几个用于结构生物学和生物医学研究的应用程序：（i）基于Java的分子图形查看器jV；（ii）显示电子密度图以评估结构质量；（iii）用于功能位点的分子表面广泛数据库eF-site，以及类似分子表面搜索服务eF-seek；（iv）识别序列和结构邻居；（v）一个带有指向上述应用程序链接的所有已知蛋白质折叠的图形用户界面Protein Globe。展示了近期的实例，突出了这些工具在识别蛋白质结构对之间的远程同源性以及为结构基因组学项目新确定的靶点赋予假定生化功能方面的效用。
