Protein Data Bank (PDB): The Single Global Macromolecular Structure Archive.
Protein Data Bank (PDB): The Single Global Macromolecular Structure Archive.
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DOI：
10.1007/978-1-4939-7000-1_26
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发表时间：
2017
期刊：
影响因子：
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通讯作者：
Velankar S
中科院分区：
文献类型：
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作者：
Burley SK;Berman HM;Kleywegt GJ;Markley JL;Nakamura H;Velankar S
蛋白质数据库（PDB）-实验确定的生物大分子及其复合物的3D结构的单一全球存储库-成立于1971年，成为生物科学中第一个开放访问的数字资源。PDB档案目前拥有约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，其中包括RCSB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）和BioMagResBank（BMRB; www.bmrb.wisc.edu）。四个wwPDB合作伙伴运营着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条目的数据沉积、生物定位和验证（deposit.wwpdb.org）。RCSB PDB目前担任档案保管员，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站点传播相同的档案数据，同时运营补充网站，提供自己对PDB数据的看法，并提供选定的增值信息和相关数据资源的链接。目前，PDB档案实验数据，相关的元数据和三维原子水平的结构模型来自三个成熟的方法：晶体学，核磁共振光谱（NMR）和电子显微镜（3DEM）。wwPDB的合作伙伴正在与相关实验领域的专家密切合作（小角散射，化学交联/质谱，福斯特能量共振转移或FRET等）。建立一个数据资源联盟，支持对综合或混合方法得出的三维结构模型和实验数据进行可持续存档和验证。
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.