PDBx/mmCIF – Protein Data Bank Exchange Dictionary and the Macromolecular Crystallographic Information Framework

The Protein Data Bank archive (PDB) is a worldwide archival repository of information about the 3D structures of proteins, nucleic acids, and complex assemblies, managed by the Worldwide PDB (wwPDB). The PDB Exchange Dictionary (PDBx) is used by the wwPDB to define data content for deposition, annotation and archiving of PDB entries. PDBx incorporates the community standard metadata representation, the Macromolecular Crystallographic Information Framework (mmCIF), orginally developed under the auspices of the International Union of Crystallography (IUCr). PDBx has been extended by the wwPDB  to include descriptions of other experimental methods that produce 3D macromolecular structure models such as Nuclear Magnetic Resonance Spectroscopy, 3D Electron Microscopy and Tomography.

Tools

PDBx/mmCIF Software Resources

Parsing, validation, and visualization tools and libraries supporting PDBx/mmCIF, the data standard used by the Worldwide Protein Data Bank.

Use Cases

Chem-BLAST

A Web-based service for searching for and visualizing chemical structures. It uses data from the Protein Data Bank that has been transformed to RDF.

Worldwide Protein Data Bank

The Protein Data Bank archive (PDB) is a worldwide archival repository of information about the 3D structures of proteins, nucleic acids, and complex assemblies. The Worldwide PDB (wwPDB) organization manages the PDB archive and ensures that the PDB is freely and publicly available to the global community.