PDBDev

PDBDev is the prototype archive of the Worldwide Protein Data Bank (wwPDB) for integrative and hybrid structures. It provides a repository for macromolecular models and their associated experimental data that are not yet deposited in the standard Protein Data Bank (PDB) because they require complex metadata and validation across multiple experimental methods.

The platform supports integrative structure determination, where information from diverse data sources—such as cryo-electron microscopy density maps, X-ray diffraction, NMR restraints, small-angle scattering, and cross-linking mass spectrometry—is combined to build models of macromolecular assemblies. PDBDev aims to capture the full spectrum of information necessary to support these models, including coordinates, restraints, experimental observations, provenance, and modelling workflows.

Data in PDBDev are represented using the mmCIF framework with extended dictionaries that accommodate spatial restraints, experimental data, component relationships, and methods used in the modelling process. Depositions are typically submitted through wwPDB member organizations (such as RCSB PDB, PDBe, and PDBj) and undergo validation and curation before public access. Each entry is accompanied by documentation and validation reports to aid interpretation and reuse.

Relation to the main PDB: PDBDev acts as a staging and development area for integrative/hybrid structures. Some entries may migrate to the standard PDB if they meet established criteria for conventional deposition, while others may remain within PDBDev to reflect the complexity of their data and models.

History and scope: PDBDev was established in the late 2010s by the wwPDB in collaboration with its global partners to support growing needs in integrative and hybrid structural biology. It serves as a centralized platform for sharing, validating, and advancing complex structural data and methodologies.