RCSB Protein Data Bank: Sustaining a living digital data resource that enables breakthroughs in scientific research and biomedical education

被引:166
作者
Burley, Stephen K. [1 ,2 ,3 ]
Berman, Helen M. [1 ]
Christie, Cole [3 ]
Duarte, Jose M. [3 ]
Feng, Zukang [1 ]
Westbrook, John [1 ]
Young, Jasmine [1 ]
Zardecki, Christine [1 ]
机构
[1] Rutgers State Univ, Inst Quantitat Biomed, Res Collaboratory Struct Bioinformat Prot Data Ba, Piscataway, NJ 08854 USA
[2] Rutgers Canc Inst New Jersey, Robert Wood Johnson Med Sch, New Brunswick, NJ 08903 USA
[3] Univ Calif San Diego, San Diego Supercomp Ctr, Res Collaboratory Struct Bioinformat Prot Data Ba, La Jolla, CA 92093 USA
基金
美国国家卫生研究院; 美国国家科学基金会;
关键词
Research Collaboratory for Structure Bioinformatics; RCSB; Protein Data Bank; PDB; Worldwide Protein Data Bank; wwPDB; PDBx; mmCIF; chemical component dictionary; crystallography; NMR spectroscopy; 3D electron microscopy; integrative; hybrid methods; data archive; macromolecular structure; biocuration; validation; metadata; FAIR principles; open access; data deposition; PDB; VALIDATION; ARCHITECTURE; RECOGNITION; SYSTEM; TOOLS; CATH;
D O I
10.1002/pro.3331
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
The Protein Data Bank (PDB) is one of two archival resources for experimental data central to biomedical research and education worldwide (the other key Primary Data Archive in biology being the International Nucleotide Sequence Database Collaboration). The PDB currently houses >134,000 atomic level biomolecular structures determined by crystallography, NMR spectroscopy, and 3D electron microscopy. It was established in 1971 as the first open-access, digital-data resource in biology, and is managed by the Worldwide Protein Data Bank partnership (wwPDB; wwpdb.org). US PDB operations are conducted by the RCSB Protein Data Bank (RCSB PDB; RCSB.org; Rutgers University and UC San Diego) and funded by NSF, NIH, and DoE. The RCSB PDB serves as the global Archive Keeper for the wwPDB. During calendar 2016, >591 million structure data files were downloaded from the PDB by Data Consumers working in every sovereign nation recognized by the United Nations. During this same period, the RCSB PDB processed >5300 new atomic level biomolecular structures plus experimental data and metadata coming into the archive from Data Depositors working in the Americas and Oceania. In addition, RCSB PDB served >1 million RCSB.org users worldwide with PDB data integrated with approximate to 40 external data resources providing rich structural views of fundamental biology, biomedicine, and energy sciences, and >600,000 PDB101.rcsb.org educational website users around the globe. RCSB PDB resources are described in detail together with metrics documenting the impact of access to PDB data on basic and applied research, clinical medicine, education, and the economy.
引用
收藏
页码:316 / 330
页数:15
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