Protein Data Bank

The Protein Data Bank is an archive of experimentally determined three-dimensional structures of proteins and other biological macromolecules, with associated experimental and descriptive data.

Protein structure: The three-dimensional arrangement of atoms in a protein, from local folding patterns to its overall shape. PDB entries encode particular experimentally observed protein structures.
PDB file format: A fixed-column text format for representing macromolecular structures and related metadata. It is the archive’s historically established format for describing atomic models.
Structural bioinformatics: The use of computational methods to analyze and compare biological macromolecular structures. PDB entries supply core data for computational structural analysis.
Walter Hamilton: A crystallographer who helped establish the Protein Data Bank and its early standards. Hamilton helped organize the archive’s founding and its initial data practices.
Open data: Data made available for access, reuse, and redistribution under defined terms. PDB structures are openly distributed for research, teaching, and software development.
Macromolecular crystallography: A method that determines molecular structures by analyzing how crystals diffract X-rays. X-ray crystallography has produced a large share of deposited PDB structures.
mmCIF: A dictionary-based file format for representing macromolecular crystallographic data and structures. The archive uses mmCIF as its comprehensive standard for structure data.
Molecular visualization: The graphical representation of molecules and their structural features. PDB coordinates can be rendered to inspect folds, ligands, and interactions.
Brookhaven National Laboratory: A U.S. research laboratory that hosted the Protein Data Bank during its early decades. The archive began at Brookhaven in 1971.
Structural genomics: A research approach that systematically determines structures across selected sets of genes or proteins. Large-scale structure determination programs substantially increased the archive’s contents.

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