RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy
- PMID: 30357411
- PMCID: PMC6324064
- DOI: 10.1093/nar/gky1004
RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy
Abstract
The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB, rcsb.org), the US data center for the global PDB archive, serves thousands of Data Depositors in the Americas and Oceania and makes 3D macromolecular structure data available at no charge and without usage restrictions to more than 1 million rcsb.org Users worldwide and 600 000 pdb101.rcsb.org education-focused Users around the globe. PDB Data Depositors include structural biologists using macromolecular crystallography, nuclear magnetic resonance spectroscopy and 3D electron microscopy. PDB Data Consumers include researchers, educators and students studying Fundamental Biology, Biomedicine, Biotechnology and Energy. Recent reorganization of RCSB PDB activities into four integrated, interdependent services is described in detail, together with tools and resources added over the past 2 years to RCSB PDB web portals in support of a 'Structural View of Biology.'
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References
-
- Bank Protein Data. Crystallography: Protein Data Bank. Nat. New Biol. 1971; 233:223–223. - PubMed
-
- Berman H.M., Henrick K., Nakamura H.. Announcing the worldwide Protein Data Bank. Nat. Struct. Biol. 2003; 10:980. - PubMed
-
- Berman H. The Protein Data Bank: a historical perspective. Acta Crystallogr. A. 2008; 64:88–95. - PubMed
-
- Burley S.K., Berman H.M., Kleywegt G.J., Markley J.L., Nakamura H., Velankar S.. Wlodawer A, Dauter Z, Jaskolski M. Protein Data Bank (PDB): The single global macromolecular structure archive. Methods in Molecular Biology: Protein Crystallography Methods and Protocols. 2017; NY: Springer; 627–641. - PMC - PubMed
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