PDB

The Protein Data Bank (PDB) is a global, open-access repository for the three-dimensional structural data of biological macromolecules, including proteins, nucleic acids, and complex assemblies. Each entry provides atomic coordinates, experimental data, and descriptive metadata that enable researchers to study molecular structure, dynamics, and function. The PDB supports data sharing and reuse across disciplines such as biochemistry, structural biology, pharmacology, and bioinformatics.

Entries are determined by experimental methods such as X-ray crystallography, nuclear magnetic resonance spectroscopy, and cryo-electron microscopy. Structures are assigned a unique four-character PDB identifier and are curated with information about resolution, method, authors, and database cross-references. The PDB collaborates with regional data centers and journals to ensure standardized deposition and dissemination.

History and governance: The PDB originated in 1971 at Brookhaven National Laboratory to archive simple protein structures and later expanded into a global resource. In 2003 the wwPDB consortium was formed to coordinate data standards and distribution across multiple centers, including RCSB PDB, PDBe, and PDBj, with the aim of maintaining a single, uniform data backbone.

Data formats and validation: The legacy PDB format uses a fixed-column text layout, while modern submissions increasingly use the PDBx/mmCIF format to accommodate larger structures and richer metadata. Submissions undergo validation and a wwPDB validation report to assess geometry, clashes, and experimental quality before release.

Access and usage: The PDB is freely accessible via partner websites such as RCSB PDB, PDBe, and PDBj, which provide search, visualization, and download tools. Researchers use the database for structural analysis, model building, and structure-based drug design, often integrating PDB data with computational workflows and modeling software.