RCSB PDB

aid: pdb
name: RCSB PDB
description: >-
  RCSB Protein Data Bank (RCSB PDB) is a scientific data resource providing free,
  open access to the 3D structural data of biological macromolecules including proteins,
  nucleic acids, and complex assemblies. It serves researchers worldwide through
  a suite of programmatic APIs covering data retrieval, full-text and attribute search,
  sequence and structure similarity search, molecular model data access, volumetric
  electron density maps, sequence coordinate alignments, and structure alignment calculations.
image: https://www.rcsb.org/img/rcsb_logo.png
url: https://raw.githubusercontent.com/api-evangelist/pdb/refs/heads/main/apis.yml
humanURL: https://www.rcsb.org
baseURL: https://data.rcsb.org
tags:
  - Structural Biology
  - Proteomics
  - Bioinformatics
  - Genomics
  - Life Sciences
  - Open Data
  - Research
  - Macromolecules
  - Crystallography
  - NMR
created: '2026-06-13'
modified: '2026-06-13'
specificationVersion: '0.19'
type: Index
position: Producer
access: Open
apis:
  - aid: pdb:rcsb-pdb-data-api
    name: RCSB PDB Data API
    description: >-
      Provides structured access to the complete RCSB PDB holdings via REST and GraphQL
      interfaces. Given a known PDB identifier, callers can retrieve rich JSON metadata
      about entries, polymer entities, non-polymer entities (ligands), polymer entity
      instances (chains), assemblies, branched entities, and chemical components. The
      REST surface mirrors an OpenAPI/ReDoc contract while the GraphQL endpoint supports
      flexible field selection and nested queries.
    humanURL: https://data.rcsb.org
    baseURL: https://data.rcsb.org/rest/v1/core
    tags:
      - Structural Biology
      - Protein Data
      - GraphQL
      - REST
      - JSON
    properties:
      - type: Documentation
        url: https://data.rcsb.org/redoc/index.html
      - type: GraphQL
        url: https://data.rcsb.org/graphql
      - type: GraphQLExplorer
        url: https://data.rcsb.org/graphiql/index.html
      - type: PythonSDK
        url: https://github.com/rcsb/py-rcsb-api
      - type: JavaScriptSDK
        url: https://github.com/rcsb/rcsb-api-tools
    contact:
      - type: Email
        url: mailto:[email protected]
      - type: MailingList
        url: mailto:[email protected]

  - aid: pdb:rcsb-pdb-search-api
    name: RCSB PDB Search API
    description: >-
      Full-featured search API for locating PDB identifiers that match complex query
      conditions. Supports text attribute searches, BLAST-like sequence similarity
      (protein, DNA, RNA), chemical small-molecule queries (formula, SMILES, InChI),
      3D structure embedding searches, sequence motif searches, structural motif searches,
      and unstructured full-text searches. Results support pagination (up to 10,000
      hits), sorting, faceted aggregations, and grouping by sequence identity or
      UniProt accession. Returns entries, assemblies, polymer entities, non-polymer
      entities, polymer instances, or chemical component identifiers.
    humanURL: https://search.rcsb.org
    baseURL: https://search.rcsb.org/rcsbsearch/v2/query
    tags:
      - Search
      - Sequence Search
      - Structure Search
      - Chemical Search
      - BLAST
      - SMILES
    properties:
      - type: Documentation
        url: https://search.rcsb.org/redoc/index.html
      - type: GettingStarted
        url: https://www.rcsb.org/docs/programmatic-access/web-apis-overview
      - type: OpenAPI
        url: openapi/rcsb-pdb-search-api.json
    contact:
      - type: Email
        url: mailto:[email protected]
      - type: MailingList
        url: mailto:[email protected]

  - aid: pdb:rcsb-pdb-model-server-api
    name: RCSB PDB ModelServer API
    description: >-
      Provides on-demand access to subsets of macromolecular model data stored in
      PDBx/mmCIF format. Callers can request individual chains, residue ranges, ligand
      environments, or symmetry-expanded assemblies without downloading full structure
      files, enabling efficient downstream visualization and analysis workflows.
    humanURL: https://models.rcsb.org
    baseURL: https://models.rcsb.org
    tags:
      - Macromolecular Models
      - mmCIF
      - Structure Coordinates
      - Subset Access
    properties:
      - type: Documentation
        url: https://models.rcsb.org
      - type: OpenAPI
        url: openapi/rcsb-pdb-model-server-api.json
    contact:
      - type: Email
        url: mailto:[email protected]

  - aid: pdb:rcsb-pdb-volume-server-api
    name: RCSB PDB VolumeServer API
    description: >-
      Delivers subsets of volumetric electron density and cryo-EM map data associated
      with PDB entries. Instead of downloading large map files, researchers can query
      a specific region around a ligand or residue and retrieve only the relevant density
      slice, accelerating interactive visualization in tools like Mol*.
    humanURL: https://maps.rcsb.org
    baseURL: https://maps.rcsb.org
    tags:
      - Electron Density
      - Cryo-EM
      - Volumetric Data
      - Maps
    properties:
      - type: Documentation
        url: https://maps.rcsb.org
      - type: OpenAPI
        url: openapi/rcsb-pdb-volume-server-api.json
    contact:
      - type: Email
        url: mailto:[email protected]

  - aid: pdb:rcsb-pdb-sequence-coordinates-api
    name: RCSB PDB Sequence Coordinates API
    description: >-
      GraphQL service providing sequence-level alignments between structural databases
      and external sequence resources. Exposes two core queries — alignment and
      annotations — enabling callers to map PDB chain positions to UniProt, NCBI
      RefSeq (protein and genomic), CATH, SCOPe, and Computed Structure Models (CSMs).
      Replaces the legacy 1D Coordinates Service.
    humanURL: https://sequence-coordinates.rcsb.org
    baseURL: https://sequence-coordinates.rcsb.org/graphql
    tags:
      - Sequence Alignment
      - UniProt
      - NCBI
      - GraphQL
      - Annotations
    properties:
      - type: Documentation
        url: https://sequence-coordinates.rcsb.org
      - type: GraphQLExplorer
        url: https://sequence-coordinates.rcsb.org/graphiql/index.html
    contact:
      - type: Email
        url: mailto:[email protected]

  - aid: pdb:rcsb-pdb-alignment-api
    name: RCSB PDB Structure Alignment API
    description: >-
      Asynchronous REST API that performs programmatic structure alignment calculations
      between PDB entries or user-supplied coordinate files. Callers submit an alignment
      job via POST /submit (accepting PDBx/mmCIF, BinaryCIF, or legacy PDB format,
      with optional gzip compression), receive a UUID ticket, and poll GET /results
      for status and output. Enables large-scale structural comparison workflows
      without manual interaction with the RCSB PDB website.
    humanURL: https://alignment.rcsb.org
    baseURL: https://alignment.rcsb.org
    tags:
      - Structure Alignment
      - Structural Comparison
      - Asynchronous
      - Computational
    properties:
      - type: Documentation
        url: https://alignment.rcsb.org/api-reference.html
      - type: QueryEditor
        url: https://alignment.rcsb.org/query-editor.html
    contact:
      - type: Email
        url: mailto:[email protected]

common:
  - type: JSONLd
    url: json-ld/pdb.json
  - type: Website
    url: https://www.rcsb.org
  - type: Documentation
    url: https://www.rcsb.org/docs/programmatic-access/web-apis-overview
  - type: GettingStarted
    url: https://www.rcsb.org/docs/programmatic-access
  - type: FileDownloads
    url: https://files.wwpdb.org
  - type: GitHub
    url: https://github.com/rcsb
  - type: PythonSDK
    url: https://github.com/rcsb/py-rcsb-api
  - type: JavaScriptSDK
    url: https://github.com/rcsb/rcsb-api-tools
  - type: StatusPage
    url: https://www.rcsb.org/pages/policies
  - type: RateLimits
    url: rate-limits/pdb-rate-limits.yml
  - type: Plans
    url: plans/pdb-plans-pricing.yml
  - type: FinOps
    url: finops/pdb-finops.yml
  - type: Contact
    url: mailto:[email protected]
  - type: MailingList
    url: https://groups.google.com/g/rcsb-pdb-api-announcements

maintainers:
  - FN: Kin Lane
    email: [email protected]