RCSB PDB website screenshot

RCSB PDB

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.

RCSB PDB publishes 4 APIs on the APIs.io network, including General API, Metadata Service API, Search Service API, and 1 more. Tagged areas include Structural Biology, Proteomics, Bioinformatics, Genomics, and Life Sciences.

RCSB PDB’s developer surface includes documentation, getting-started guide, GitHub presence, and 13 more developer resources.

🌐 Visit website 📡 Source on GitHub
33.7/100 thin ▬ flat Agent 26/100 agent aware saas Full breakdown ↓
scored 2026-09-08 · rubric v0.20.0
AccessFree
3 APIs
Structural BiologyProteomicsBioinformaticsGenomicsLife SciencesOpen DataResearchMacromoleculesCrystallographyNMR

Kin Score

Kin Score Kin Score How this is scored →
scored 2026-09-08 · rubric v0.20.0
Composite quality — 33.7/100 · thin
Contract Quality 8.9 / 19
Developer Ergonomics 3.2 / 15
Access Clarity 4.3 / 15
Operational Transparency 5.1 / 10
Contract Governance 0.0 / 9
Discoverability 5.6 / 8
Regulatory Posture 1.1 / 15
Create-or-Update Ergonomics 0.0 / 10
Agent readiness — 26/100 · agent aware
Machine-Readable Contract 18 / 18
Agentic Access Contract 10 / 10
Documented Reversibility 0 / 6
MCP Server 0 / 12
Machine-Readable Auth 0 / 10
Idempotency 0 / 9
Stable Error Semantics 8 / 8
Request/Response Examples 7 / 7
Rate-Limit Signaling 7 / 7
Typed Event Surface 0 / 6
Agent Skills 0 / 5
Well-Known Catalog 0 / 4
Consent & Bot Identity 0 / 3
A2A Agent Card 0 / 8
Dry-Run / Simulate Mode 0 / 4
Delegated User Identity 0 / 6
Protected Resource Metadata 0 / 5
Registration Without a Human 0 / 6
Agentic Commerce Well-Known Document 0 / 5
Regulatory Posture applies to this provider. Its tags matched the Health regime, so Regulatory Posture carries 15 points of the composite. If this regime is wrong for your business, say so on your provider repo — the applicability map is public and we will correct it.
Create-or-Update Ergonomics applies to this provider. This API accepts writes, so it carries 10 points of the composite. It is scored from the published contracts themselves: whether a caller can create-or-update in one call, whether the write accepts a key the caller already holds, and whether the response says which branch ran. Without that, every write needs a search-and-branch in front of it, and the first time that check is skipped a duplicate record is created. Scored against the observed mean rather than raw — a provider at the catalog average is unchanged by this facet, not penalised by it.
The six quality facets above are damped to 75 points between them, because the conditional facet above carries the other 25. That is why each facet's contribution is shown against a damped maximum: raising a quality facet moves the composite by 75% of its nominal weight, not 100%. The full arithmetic is at apis.io/rating/.
Improve this rating by publishing the missing artifacts — every area above can be raised, and the full rubric is at apis.io/rating/. Every facet and dimension name above is a link: it opens that measurement's own page — what it means, the exact checks that feed it, how the whole catalog distributes on it, and the providers at the top of it. This rating is computed from github.com/api-evangelist/pdb: open an issue to ask a question, or submit a pull request to add artifacts. Submit an artifact on GitHub — free → Manage your own listing — the Influence plan, $499/mo →

APIs 7

Individual APIs this provider publishes, each with its own machine-readable definition.

RCSB PDB Data API

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...

RCSB PDB Sequence Coordinates API

GraphQL service providing sequence-level alignments between structural databases and external sequence resources. Exposes two core queries — alignment and annotations — enabling...

RCSB PDB Structure Alignment API

Asynchronous REST API that performs programmatic structure alignment calculations between PDB entries or user-supplied coordinate files. Callers submit an alignment job via POST...

RCSB PDB General API

The General API from RCSB PDB — 12 operation(s) for general.

RCSB PDB Metadata Service API

The Metadata Service API from RCSB PDB — 3 operation(s) for metadata service.

RCSB PDB Search Service API

The Search Service API from RCSB PDB — 2 operation(s) for search service.

RCSB PDB Suggest Service API

The Suggest Service API from RCSB PDB — 1 operation(s) for suggest service.

Scroll for all 7

Open Collections 5

Open, tool-agnostic API collections (OpenAPI-derived and Bruno).

API Collection

OPEN COLLECTION

ModelServer General API

OPEN COLLECTION

ModelServer General Metadata Service API

OPEN COLLECTION

ModelServer General Search Service API

OPEN COLLECTION

ModelServer General Suggest Service API

OPEN COLLECTION

GraphQL 1

GraphQL schemas published by this provider.

RCSB Protein Data Bank GraphQL API

The RCSB PDB GraphQL API provides flexible, field-selective access to the complete structural biology holdings of the Protein Data Bank. Callers can retrieve richly nested metad...

GRAPHQL

Pricing Plans 1

Published pricing tiers and plan structures.

Pdb Plans Pricing

1 plans

PLANS

Rate Limits 1

Documented rate limits and quota policies.

Pdb Rate Limits

7 limits

RATE LIMITS

FinOps 1

Cost, billing, and metering signals for API financial operations.

Pdb Finops

FINOPS

Security Posture 1

Authentication, domain security, vulnerability disclosure, and trust-center signals.

Pdb Domain Security

TLSv1.3 · HSTS · DMARC

SECURITY

Agentic Access 1

Recommended x-agentic-access execution contracts for AI agents.

Pdb Agentic Access

28 operations · 10 acting

28 operations · 10 acting

AGENTIC

Resources

Get Started 1

Portal, sign-up, and the first successful call

GettingStarted
GettingStarted

Documentation 1

Reference material describing how the API behaves

Documentation
Documentation

Agent Surfaces 1

MCP servers, agent skills, and machine-readable catalogs

AgenticAccess
AgenticAccess

Design & Contract 1

Pagination, idempotency, versioning, errors, and events

JSONLD
JSONLD

Build 3

SDKs, sample code, and the tooling you integrate with

GitHub
GitHub
 PythonSDK
PythonSDK
 JavaScriptSDK
JavaScriptSDK

Access & Security 1

Authentication, authorization, and security posture

DomainSecurity
DomainSecurity

Operate 3

Status, limits, changes, and where to get help

StatusPage
StatusPage
 RateLimits
RateLimits
 Contact
Contact

Commercial 2

Pricing, plans, and the legal terms of use

Plans
Plans
 FinOps
FinOps

Company 1

The organization behind the API

Website
Website

Other 2

Properties that don't map to a standard resource type

FileDownloads
FileDownloads
 MailingList
MailingList

Source (apis.yml)

apis.yml Raw ↑ 
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.
deliveryModel:
  model: saas
  open_source: false
  commercial: true
  callable_host: true
  label: Hosted service · you call their endpoint
  confidence: high
  source:
  - openapi
  - pricing
  generated: '2026-08-28'
  method: derived
accessModel:
  pricing: free
  onboarding: unknown
  trial: false
  try_now: false
  public: false
  label: Free
  confidence: medium
  source:
  - plans
  generated: '2026-07-22'
  method: derived
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: '0.23'
type: Index
position: Producing
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
  - type: GraphQLSchema
    url: graphql/pdb-schema.graphql
  - type: GraphQLDocumentation
    url: graphql/pdb-graphql.md
  contact:
  - type: Email
    url: mailto:info@rcsb.org
  - type: MailingList
    url: mailto:api+subscribe@rcsb.org
- 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:info@rcsb.org
- 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:info@rcsb.org
- aid: pdb:pdb-general-api
  name: RCSB PDB General API
  description: The General API from RCSB PDB — 12 operation(s) for general.
  humanURL: https://data.rcsb.org
  baseURL: https://data.rcsb.org/rest/v1/core
  tags: []
  tags_raw:
  - General
  properties:
  - type: OpenAPI
    url: openapi/pdb-general-api-openapi.yml
  - type: Documentation
    url: https://search.rcsb.org/redoc/index.html
  - type: GettingStarted
    url: https://www.rcsb.org/docs/programmatic-access/web-apis-overview
  - type: Documentation
    url: https://models.rcsb.org
  - type: Documentation
    url: https://maps.rcsb.org
- aid: pdb:pdb-metadata-service-api
  name: RCSB PDB Metadata Service API
  description: The Metadata Service API from RCSB PDB — 3 operation(s) for metadata service.
  humanURL: https://data.rcsb.org
  baseURL: https://data.rcsb.org/rest/v1/core
  tags:
  - Metadata Service
  properties:
  - type: OpenAPI
    url: openapi/pdb-metadata-service-api-openapi.yml
  - type: Documentation
    url: https://search.rcsb.org/redoc/index.html
  - type: GettingStarted
    url: https://www.rcsb.org/docs/programmatic-access/web-apis-overview
  - type: Documentation
    url: https://models.rcsb.org
  - type: Documentation
    url: https://maps.rcsb.org
- aid: pdb:pdb-search-service-api
  name: RCSB PDB Search Service API
  description: The Search Service API from RCSB PDB — 2 operation(s) for search service.
  humanURL: https://data.rcsb.org
  baseURL: https://data.rcsb.org/rest/v1/core
  tags:
  - Search Service
  properties:
  - type: OpenAPI
    url: openapi/pdb-search-service-api-openapi.yml
  - type: Documentation
    url: https://search.rcsb.org/redoc/index.html
  - type: GettingStarted
    url: https://www.rcsb.org/docs/programmatic-access/web-apis-overview
  - type: Documentation
    url: https://models.rcsb.org
  - type: Documentation
    url: https://maps.rcsb.org
- aid: pdb:pdb-suggest-service-api
  name: RCSB PDB Suggest Service API
  description: The Suggest Service API from RCSB PDB — 1 operation(s) for suggest service.
  humanURL: https://data.rcsb.org
  baseURL: https://data.rcsb.org/rest/v1/core
  tags:
  - Suggest Service
  properties:
  - type: OpenAPI
    url: openapi/pdb-suggest-service-api-openapi.yml
  - type: Documentation
    url: https://search.rcsb.org/redoc/index.html
  - type: GettingStarted
    url: https://www.rcsb.org/docs/programmatic-access/web-apis-overview
  - type: Documentation
    url: https://models.rcsb.org
  - type: Documentation
    url: https://maps.rcsb.org
common:
- type: AgenticAccess
  url: agentic-access/pdb-agentic-access.yml
- type: DomainSecurity
  url: security/pdb-domain-security.yml
- 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:info@rcsb.org
- type: MailingList
  url: https://groups.google.com/g/rcsb-pdb-api-announcements
maintainers:
- FN: Kin Lane
  email: kin@apievangelist.com

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