RCSB PDB Help

Web Services Overview

Data API

All static data that is exposed in rcsb.org is available in the Data API. The schema follows the mmCIF dictionary, extended with annotations coming from external resources. The core PDB data is split up into core objects, one per level of the structural data hierarchy, with entity subdivided into polymeric and non-polymeric subschemas (differing from the mmCIF dictionary). These are some of the core objects:

core_entry: data that relates to a PDB entry. Identified by a 4 letter pdb_id.
core_polymer_entity: data for each polymeric molecular entity in a PDB entry. Identified by a _
core_nonpolymer_entity: data for each non-polymeric molecular entity in a PDB entry. Identified by a _
core_assembly: data for each biological assembly in a PDB entry. Identified by a -
core_polymer_entity_instance: an instance of a certain polymeric molecular entity, also known as chain. Identified by a .
core_chem_comp: a chemical component. Identified by a 3-letter chem_comp_id

Both internal additions to the mmCIF dictionary and external resources annotations are prefixed with rcsb_. In each core object, the rcsb_<core_object>_container_identifiers field holds the cardinal identifiers for the objects and any parent/child. Additionally every core object contains a single string identifier in field rcsb_id.

The data is available via 2 different interfaces:

REST API Full Reference

The REST API permits the retrieval of all data for one core object at a time.

GraphQL API (GraphiQL interface)

The GraphQL interface offers more flexible data retrieval, essentially making it possible to grab any piece of data from any level of the hierarchy in a single query. To use it programmatically POST your GraphQL queries under the data.rcsb.org/graphql endpoint.

All output from both REST and GraphQL interfaces is offered in JSON format.

Data API Tutorial

Search API

The search API programmatically exposes all search functionality available at rcsb.org. It is possible to perform queries with arbitrary Boolean logic across all data available in the RCSB PDB data API via a convenient JSON-format query language. At the root level it is also possiblen to combine text-based searches (any text/numerical field in the RCSB PDB data API) with protein/nucleotide sequence search (mmseqs2 software) and Structure similarity searches (BioZernike software, described in Guzenko et al 2020). All output from the Search API is offered in JSON format.

Search API Tutorial

Search API Full Reference

ModelServer API

The ModelServer is a service for accessing subsets of macromolecular model data. It delivers atomic coordinates together with annotations in the primary data files in a compressed BinaryCIF encoding (BCIF). Structure data can be served at different levels of granularity (e.g., assembly, polymer chain, ligand), and ligand data may also be delivered in popular chemical informatics formats (e.g., SDF, MOL, MOL2).

ModelServer API Specification

The specification of the BinaryCIF format can be found at: https://github.com/molstar/BinaryCIF.

VolumeServer API

The VolumeServer is a service for accessing subsets of volumetric data. It automatically downsamples the data depending on the volume of the requested region to reduce the bandwidth requirements and provide near-instant access to even the largest data sets.

VolumeServer API Specification

Both ModelServer and VolumeServer are part of Mol* (D. Sehnal, A.S. Rose, J. Kovca, S.K. Burley, S. Velankar (2018) Mol*: Towards a common library and tools for web molecular graphics MolVA/EuroVis Proceedings.doi:10.2312/molva.20181103).

1D Coordinate Server

The RCSB PDB 1D Coordinate Server compiles alignments between structural and sequence databases and integrates protein positional features from multiple resources. Alignment data is available for NCBI RefSeq (including protein and genomic sequences), UniProt and PDB sequences. Protein positional features are integrated from UniProt, CATH, SCOPe and RCSB PDB and collected from the RCSB PDB Data Warehouse.