International open access database of large biological molecules
Protein Data Bank
Content
Description
Protein structure
X-ray crystallography
NMR Structure Determination
Contact
Primary citation
PMID 30357364
Access
Data format
mmCIF, PDB
Website
www.wwpdb.org
ebi.ac.uk
www.rcsb.org
bmrb.io
pdbj.org
The Protein Data Bank (PDB)[1] is a database for the three-dimensional structural data of large biological molecules such as proteins and nucleic acids, which is overseen by the Worldwide Protein Data Bank (wwPDB). These structural data are obtained and deposited by biologists and biochemists worldwide through the use of experimental methodologies such as X-ray crystallography, NMR spectroscopy, and, increasingly, cryo-electron microscopy. All submitted data are reviewed by expert biocurators and, once approved, are made freely available on the Internet under the CC0 Public Domain Dedication.[2] Global access to the data is provided by the websites of the wwPDB member organisations (PDBe,[3] PDBj,[4] RCSB PDB,[5] and BMRB[6]).
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, SCOP and CATH classify protein structures, while PDBsum provides a graphic overview of PDB entries using information from other sources, such as Gene Ontology.[7][8]
^wwPDB, Consortium (2019). "Protein Data Bank: the single global archive for 3D macromolecular structure data". Nucleic Acids Res. 47 (D1): 520–528. doi:10.1093/nar/gky949. PMC 6324056. PMID 30357364.
^"Protein Data Bank Japan – PDB Japan – PDBj". pdbj.org.
^Bank, RCSB Protein Data. "RCSB PDB: Homepage". rcsb.org.
^Cite error: The named reference :0 was invoked but never defined (see the help page).
^Berman, H. M. (January 2008). "The Protein Data Bank: a historical perspective" (PDF). Acta Crystallographica Section A. A64 (1): 88–95. doi:10.1107/S0108767307035623. PMID 18156675.
^Laskowski RA, Hutchinson EG, Michie AD, Wallace AC, Jones ML, Thornton JM (December 1997). "PDBsum: a Web-based database of summaries and analyses of all PDB structures". Trends Biochem. Sci. 22 (12): 488–90. doi:10.1016/S0968-0004(97)01140-7. PMID 9433130.
The ProteinDataBank (PDB) is a database for the three-dimensional structural data of large biological molecules such as proteins and nucleic acids, which...
period. Data repository List of databases Star Wars Databank ProteinDataBank National Trauma DataBank Memory bank International Tree-Ring DataBank Hazardous...
of a protein. The ProteinDataBank (PDB) was established in 1971 as the central archive of all experimentally determined protein structure data. Today...
representing macromolecular structure data, developed by the International Union of Crystallography (IUCr) and the ProteinDataBank It is an extension of the Crystallographic...
contact determination. The ProteinDataBank (PDB) is a database of 3D structure data for large biological molecules, such as proteins, DNA, and RNA. PDB is...
Bradley AR, Christie CH, et al. (January 2017). "The RCSB proteindatabank: integrative view of protein, gene and 3D structural information". Nucleic Acids...
knowing the protein's primary structure and comparing the possible predicted tertiary structure with known tertiary structures in proteindatabanks. This only...
the contents of each 3D macromolecular structure deposited in the ProteinDataBank (PDB). The original version of the database was developed around 1995...
atomic numbers) and cartesian coordinates. The ProteinDataBank Format is commonly used for proteins but is also used for other types of molecules. There...
data center within the Worldwide ProteinDataBank (wwPDB) partnership. As the designated Archive Keeper, RCSB PDB ensures the security of PDB data and...
curated list of selected transmembrane proteins from the ProteinDataBank MemProtMD - a database of membrane protein structures simulated by coarse-grained...
ProteinDataBank (PDB) file, interacting with Jmol and many more. This application programming interface (API) provides various file parsers, data models...
ProteinDataBank contains 181,018 X-ray, 19,809 EM [definition needed]and 12,697 NMR[definition needed] protein structures. The number of proteins encoded...
experimentally measured binding affinity data (Kd, Ki, and IC50) for the protein-ligand complexes deposited in the ProteinDataBank (PDB). It thus provides a link...
explore biological macromolecule structures, such as those found in the ProteinDataBank (PDB). It was originally developed by Roger Sayle in the early 1990s...
The Protein Circular Dichroism DataBank (PCDDB) is a database of circular dichroism and synchrotron radiation. Circular dichroism Synchrotron Radiation...
activator. Three-dimensional protein structures of the peroxidated catalase intermediates are available at the ProteinDataBank. Hydrogen peroxide is a harmful...
in specialised contexts. In the description of protein structure, in particular in the ProteinDataBank file format, a heteroatom record (HETATM) describes...
addition, structures of many water-soluble protein domains of IMPs are available in the ProteinDataBank. Their membrane-anchoring α-helices have been...
difference between large numbers. Around 90% of the protein structures available in the ProteinDataBank have been determined by X-ray crystallography. This...
digital repository managers, data center staff, and others who collect, manage, and store digital information. The ProteinDataBank was established in 1971...
that generates schematic 2-D representations of protein-ligand complexes from standard ProteinDataBank file input. The LIGPLOT is used to generate images...
arrangement of transmembrane and peripheral proteins in membranes. Proteins structures are taken from the ProteinDataBank. OPM also provides structural classification...
weight of R-PE is 250,000 daltons. Crystal structures available in the ProteinDataBank contain in one (αβ)2 or (αβγ)2 asymmetric unit of different phycoerythrins:...
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