Burley Stephen K, Berman Helen M, Kleywegt Gerard J, Markley John L, Nakamura Haruki, Velankar Sameer
Research Collaboratory for Structural Bioinformatics Protein Data Bank, Center for Integrative Proteomics, Research, Institute for Quantitative Biomedicine, and Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA.
Rutgers Cancer Institute of New Jersey, Robert Wood Johnson Medical School, New Brunswick, NJ, 08903, USA.
Methods Mol Biol. 2017;1607:627-641. doi: 10.1007/978-1-4939-7000-1_26.
The Protein Data Bank (PDB)--the single global repository of experimentally determined 3D structures of biological macromolecules and their complexes--was established in 1971, becoming the first open-access digital resource in the biological sciences. The PDB archive currently houses ~130,000 entries (May 2017). It is managed by the Worldwide Protein Data Bank organization (wwPDB; wwpdb.org), which includes the RCSB Protein Data Bank (RCSB PDB; rcsb.org), the Protein Data Bank Japan (PDBj; pdbj.org), the Protein Data Bank in Europe (PDBe; pdbe.org), and BioMagResBank (BMRB; www.bmrb.wisc.edu). The four wwPDB partners operate a unified global software system that enforces community-agreed data standards and supports data Deposition, Biocuration, and Validation of ~11,000 new PDB entries annually (deposit.wwpdb.org). The RCSB PDB currently acts as the archive keeper, ensuring disaster recovery of PDB data and coordinating weekly updates. wwPDB partners disseminate the same archival data from multiple FTP sites, while operating complementary websites that provide their own views of PDB data with selected value-added information and links to related data resources. At present, the PDB archives experimental data, associated metadata, and 3D-atomic level structural models derived from three well-established methods: crystallography, nuclear magnetic resonance spectroscopy (NMR), and electron microscopy (3DEM). wwPDB partners are working closely with experts in related experimental areas (small-angle scattering, chemical cross-linking/mass spectrometry, Forster energy resonance transfer or FRET, etc.) to establish a federation of data resources that will support sustainable archiving and validation of 3D structural models and experimental data derived from integrative or hybrid methods.
蛋白质数据库（PDB）——全球唯一的生物大分子及其复合物三维结构实验测定结果的储存库——成立于1971年，成为生命科学领域首个开放获取的数字资源。PDB档案库目前存有约130,000个条目（2017年5月）。它由全球蛋白质数据库组织（wwPDB；wwpdb.org）管理，该组织包括美国结构生物信息学合作研究协会蛋白质数据库（RCSB PDB；rcsb.org）、日本蛋白质数据库（PDBj；pdbj.org）、欧洲蛋白质数据库（PDBe；pdbe.org）以及生物磁共振数据库（BMRB；www.bmrb.wisc.edu）。wwPDB的四个合作伙伴运行一个统一的全球软件系统，该系统执行社区商定的数据标准，并支持每年约11,000个新PDB条目的数据提交、生物注释和验证（deposit.wwpdb.org）。RCSB PDB目前担任档案保管人，确保PDB数据的灾难恢复并协调每周更新。wwPDB合作伙伴从多个FTP站点分发相同的存档数据，同时运营互补网站，这些网站提供PDB数据的自有视图以及选定的增值信息和相关数据资源链接。目前，PDB存档实验数据、相关元数据以及源自三种成熟方法的三维原子水平结构模型：晶体学、核磁共振光谱法（NMR）和电子显微镜（3DEM）。wwPDB合作伙伴正在与相关实验领域（小角散射、化学交联/质谱、荧光共振能量转移或FRET等）的专家密切合作，以建立一个数据资源联盟，该联盟将支持对三维结构模型以及源自整合或混合方法的实验数据进行可持续存档和验证。
