PDB (RCSB)

What PDB (RCSB) is

The RCSB Protein Data Bank (RCSB PDB) is a database of three-dimensional macromolecular structures and an organisation within the Worldwide PDB (wwPDB) partnership. It provides access to experimentally determined biological structures, which serve as a reference standard for training and validating computational models in structural biology.

The resource addresses the need to archive, search, and analyse macromolecular assemblies and their chemical components. In addition to experimental entries, it makes computed structure models and integrative structures available, alongside tools that connect structural data to genomic references, functional annotations, and small-molecule chemical representations.

How it is organised

RCSB PDB archives atomic coordinates and experimental data using the PDBx/mmCIF format and extended PDB identifiers. Entries comprise experimentally determined structures, integrative structures, and computed structure models sourced from AlphaFoldDB and ModelArchive. The platform exposes programmatic access through application programming interfaces (APIs) and a Model Context Protocol (MCP) server for artificial intelligence workflows.

The database integrates analytical tools across sequence, structure, and chemical domains. Sequence similarity searches run via the MMseqs2 method, small molecules are indexed and queried using SMILES, InChI, or chemical formulas, and three-dimensional shape searches are computed using machine learning vector embeddings. Users can also perform pairwise coordinate alignments, search for catalytic or binding 3D motifs, map sequences to UniProtKB entries and genomic data, and query structural attributes using boolean logic.

Key facts

What you can use it for

Structure comparison and motif identification

Researchers can compute pairwise structural alignments, retrieve assemblies with similar geometric shapes using vector embeddings, or locate spatial motifs corresponding to catalytic and binding sites.

Sequence and chemical searching

Users can identify proteins or nucleic acids matching specific sequences via MMseqs2, find biological sequence motifs, or query co-crystallised ligands and small molecules using SMILES, InChI, or formulas.

Cross-database annotation mapping

Biologists can map structural features directly onto protein assemblies, examine links to UniProtKB annotations, and inspect relationships between PDB entities, genes, and genomes.

Machine learning model development

Computational researchers use the experimentally determined macromolecular structures as a gold standard for training and validating predictive algorithms.

Query it here

The research agent queries PDB (RCSB) directly — no account, no API key — and every answer links back to the record it came from. Ask in plain language and it writes the query.

Strengths and limits

Questions