What Is PDB (Protein Data Bank)

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∟What Is PDB (Protein Data Bank)

This section provides a quick introduction of the PDB (Protein Data Bank), which is a database for the three-dimensional structural data of large biological molecules, such as proteins and nucleic acids.

What Is PDB (Protein Data Bank)? - The Protein Data Bank (PDB) is a database for the three-dimensional structural data of large biological molecules, such as proteins and nucleic acids. The data, typically obtained by X-ray crystallography, NMR spectroscopy, or, increasingly, cryo-electron microscopy, and submitted by biologists and biochemists from around the world, are freely accessible on the Internet via the websites of its member organizations (PDBe, PDBj, RCSB, and BMRB). The PDB is overseen by an organization called the Worldwide Protein Data Bank, wwPDB.

PDB related Websites include:

http://www.wwpdb.org - Website for the Worldwide PDB (wwPDB) organization which manages the PDB archive and ensures that the PDB is freely and publicly available to the global community.
http://www.rcsb.org - Website for the RCSB PDB (Research Collaboratory for Structural Bioinformatics Protein Data Bank), which provides simple and advanced searching for macromolecules and ligands, tabular reports, specialized visualization tools, sequence-structure comparisons, RCSB PDB Mobile, Molecule of the Month and other educational resources at PDB-101, and more.
https://www.ebi.ac.uk/pdbe/ - Website for the PBDe (Protein Data Bank in European), which provides rich information about all PDB entries, multiple search and browse facilities, advanced services including PDBePISA, PDBeFold and PDBeMotif, advanced visualization and validation of NMR and EM structures, tools for bioinformaticians.
https://pdbj.org - Website for the PBDj (Protein Data Bank Japan) which supports browsing in multiple languages such as Japanese, Chinese, and Korean; SeSAW identifies functionally or evolutionarily conserved motifs by locating and annotating sequence and structural similarities, tools for bioinformaticians, and more.
http://www.bmrb.wisc.edu - Website for the BMRB (Biological Magnetic Resonance Data Bank), which Collects NMR (Nuclear Magnetic Resonance) data from any experiment and captures assigned chemical shifts, coupling constants, and peak lists for a variety of macromolecules; contains derived annotations such as hydrogen exchange rates, pKa values, and relaxation parameters.