Editing Protein Data Bank (section)

{{short description|International open access database of large biological molecules}}
{{infobox biodatabase
|title = Protein Data Bank
|logo = [[File:Wwpdb-logo.png|200px]]
|description = {{unbulleted list | [[Protein structure]] | [[X-ray crystallography]] | [[Nuclear magnetic resonance spectroscopy of proteins|NMR Structure Determination]]}}
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|pmid = 30357364
|released =
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|format = [[mmCIF]], [[Protein Data Bank (file format)|PDB]]
|url = {{Plainlist|
* {{URL|https://www.wwpdb.org/}}
* {{URL|https://www.ebi.ac.uk/pdbe/|ebi.ac.uk}}
* {{URL|https://www.rcsb.org}}
* {{URL|https://bmrb.io/}}
* {{URL|https://pdbj.org/}}
}}
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The '''Protein Data Bank''' ('''PDB''')<ref>{{cite journal
|pmid=30357364 
|pmc=6324056 
 | first = Consortium 
 | last = wwPDB
 | year = 2019
 | title = Protein Data Bank: the single global archive for 3D macromolecular structure data
 | journal = Nucleic Acids Res.
 | volume = 47
 | issue = D1
 | pages = 520–528
 | doi =  10.1093/nar/gky949
 }}</ref> is a [[database]] for the three-dimensional structural data of large biological molecules such as [[protein]]s and [[nucleic acid]]s, which is overseen by the [[Worldwide Protein Data Bank]] (wwPDB). This structural data is obtained and deposited by [[biologist]]s and [[biochemist]]s worldwide through the use of experimental methodologies such as [[X-ray crystallography]], [[Nuclear magnetic resonance spectroscopy of proteins|NMR spectroscopy]], and, increasingly, [[cryo-electron microscopy]]. All submitted data are reviewed by expert [[Biocuration|biocurators]] and, once approved, are made freely available on the Internet under the CC0 Public Domain Dedication.<ref>{{Cite web |last=wwPDB.org |title=wwPDB: Usage Policies |url=https://www.wwpdb.org/about/usage-policies |access-date=2024-04-16 |website=www.wwpdb.org |language=en}}</ref> Global access to the data is provided by the websites of the wwPDB member organizations (PDBe,<ref name=autogenerated1>{{cite web|url=http://www.pdbe.org/|title=PDBe home < Node < EMBL-EBI |website= pdbe.org}}</ref> PDBj,<ref name=autogenerated2>{{cite web|url=http://www.pdbj.org/|title=Protein Data Bank Japan – PDB Japan – PDBj|website= pdbj.org}}</ref> RCSB PDB,<ref>{{cite web| url= http://www.rcsb.org/| title=RCSB PDB: Homepage|first=RCSB Protein Data|last=Bank|website= rcsb.org}}</ref> and BMRB<ref name=":0" />).

The PDB is a key in areas of [[structural biology]], such as [[structural genomics]]. Most major scientific journals and some funding agencies now require scientists to submit their structure data to the PDB. Many other databases use protein structures deposited in the PDB. For example, [[Structural Classification of Proteins database|SCOP]] and [[CATH]] classify protein structures, while [[PDBsum]] provides a graphic overview of PDB entries using information from other sources, such as [[Gene Ontology]].<ref name = "Historical">{{cite journal | first = H. M.  | last = Berman|date=January 2008 | title = The Protein Data Bank: a historical perspective | pmid = 18156675| journal = Acta Crystallographica Section A  | volume = A64 | issue = 1 | pages = 88–95| doi = 10.1107/S0108767307035623| url = http://journals.iucr.org/a/issues/2008/01/00/sc5004/sc5004.pdf| doi-access = free}}</ref><ref name="pmid9433130">{{cite journal |vauthors= Laskowski RA, Hutchinson EG, Michie AD, Wallace AC, Jones ML, Thornton JM | title = PDBsum: a Web-based database of summaries and analyses of all PDB structures | journal = Trends Biochem. Sci. | volume = 22 | issue = 12 | pages = 488–90 | date = December 1997 | pmid = 9433130 | doi = 10.1016/S0968-0004(97)01140-7 }}</ref>