Data Rcsb RCSB RESTful API
68
AI ReadinessAI-Aware (B+)68/100
Agent-ready OpenAPI document · curated by JenticHealthcareClinical Datanone39 EndpointsREST
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For Agents
Retrieve protein structures, chemical components, polymer entities, interfaces, and groups from the RCSB Protein Data Bank for research and drug discovery workflows.
Use for: I want to retrieve a protein structure by its PDB ID, Get the assembly information for a specific structure, Look up the chemical component for a ligand, Find the DrugBank annotations for a chemical component
Not supported: Does not handle protein sequence search, structure prediction, or molecular dynamics simulation - use for retrieving published RCSB Protein Data Bank entries, entities, chemical components, interfaces, and groups only.
Jentic publishes the only available OpenAPI specification for the RCSB RESTful API, keeping it validated and agent-ready. The Research Collaboratory for Structural Bioinformatics (RCSB) Protein Data Bank exposes structured access to the canonical archive of three-dimensional macromolecular structures used in life sciences research and drug discovery. The 39-endpoint API covers entries, assemblies, polymer and non-polymer entities, entity instances, chemical components, interfaces, groups, schema, and repository holdings. Endpoints are public and require no authentication.
Install Jentic One Beta
Connect the RCSB RESTful API to your agent
Jentic One is a self-hosted execution layer for AI agents. It lets your agent call the RCSB RESTful API, or any other public or private API you need. You set the rules, the agent never sees your credentials, and every call is logged.
Two steps, two machines. Install the instance in a safe environment, then register your agent from wherever it runs.
1
Step 1: Jentic One Host machine
# On the machine that will host your Jentic One instance:
curl -fsSL "https://jentic.com/install.sh?src=apis&api=%2Fapis%2Fdata.rcsb.org%2Frcsb" | sh2
Step 2: Agent machine
# On the machine where your agent runs (keep this separate from the instance):
curl -fsSL "https://jentic.com/install.sh?src=apis&api=%2Fapis%2Fdata.rcsb.org%2Frcsb" | sh
jentic register # connects your agent to your Jentic One instanceJentic One is in public beta. The setup above keeps your agent separate from the instance, which is what you want before using real credentials: an agent running as the same OS user as Jentic One can read its stored keys directly. Just evaluating? A single local install is fine to start. See the secure deployment guide for the tiers.
Capabilities
What an agent can do with RCSB RESTful API.
Retrieve a structure entry by PDB entry ID
Fetch assembly descriptions for a given entry and assembly ID
Retrieve polymer, non-polymer, and branched entity records by entry and entity ID
Retrieve entity instance descriptions by entry and asym ID
Look up chemical components, including DrugBank annotations, by component ID
Describe pairwise polymeric interfaces by entry, assembly, and interface ID
Aggregate entries or non-polymer entities into groups by deposition or component ID
Use Cases
Patterns agents use RCSB RESTful API for, with concrete tasks.
★ Structure Retrieval for Drug Discovery
Pull protein structure metadata directly from the canonical PDB archive when running computational drug discovery pipelines. GET /core/entry/{entry_id} returns the entry, and GET /core/assembly/{entry_id}/{assembly_id} returns the biological assembly detail. Suitable for research teams in pharma, biotech, and academic labs that need programmatic access to PDB entries.
Fetch the PDB entry '6VXX' via GET /core/entry/{entry_id} and its assembly 1 via GET /core/assembly/{entry_id}/{assembly_id} and return the title and resolution.
Ligand and Chemical Component Lookups
Resolve chemical component identifiers to their full RCSB record including DrugBank annotations. GET /core/chemcomp/{comp_id} returns the chemical component definition, and GET /core/drugbank/{comp_id} returns DrugBank-derived annotations when available. Useful for cheminformatics workflows mapping ligands to drugs.
Look up CCD ID 'ATP' via GET /core/chemcomp/{comp_id} and return the chemical name, formula, and any DrugBank annotations from GET /core/drugbank/{comp_id}.
Interface and Entity Analysis
Drive interface analysis pipelines by retrieving pairwise polymeric interfaces and the polymer entities they connect. GET /core/interface/{entry_id}/{assembly_id}/{interface_id} returns the interface description, while polymer entity endpoints provide entity-level metadata. Useful for structural biology teams studying protein-protein interactions.
Retrieve the interface description for entry '1A2K' assembly 1 interface 1, then fetch the polymer entities involved to summarise the interaction.
Group-Based Aggregation Queries
Aggregate structures by deposition group or non-polymer entity group to study related entries together. GET /core/entry_groups/{group_id} returns entries by PDB Group Deposition ID, and GET /core/nonpolymer_entity_groups/{group_id} returns non-polymer entities grouped by chemical component. Useful for structural genomics consortia and curation teams.
Fetch the entry group for a PDB Group Deposition ID and produce a list of member entry IDs with their resolutions.
Agent-Driven Structural Biology Tools via Jentic
AI agents that draft research summaries or feed structure data into modelling tools can call RCSB through Jentic without managing endpoint URLs by hand. The agent searches Jentic for the relevant intent, loads the schema, and executes entry, assembly, or chemical component lookups. The endpoints are public, so Jentic mediates discovery and parameter shaping.
Use Jentic to search 'get a pdb entry', load GET /core/entry/{entry_id}, and execute it with the entry ID supplied by the user.
Key Endpoints
39 endpoints — jentic publishes the only available openapi specification for the rcsb restful api, keeping it validated and agent-ready.
METHOD
PATH
DESCRIPTION
GET
/core/entry/{entry_id}
Get a structure entry by entry ID
GET
/core/assembly/{entry_id}/{assembly_id}
Get a structural assembly by entry and assembly ID
GET
/core/chemcomp/{comp_id}
Get a chemical component by CCD ID
GET
/core/drugbank/{comp_id}
Get DrugBank annotations for a chemical component
GET
/core/interface/{entry_id}/{assembly_id}/{interface_id}
Get a pairwise polymeric interface description
GET
/core/entry_groups/{group_id}
Get an aggregated entry group
GET
/core/branched_entity/{entry_id}/{entity_id}
Get a branched entity by entry and entity ID
GET
/core/entry/{entry_id}
Get a structure entry by entry ID
GET
/core/assembly/{entry_id}/{assembly_id}
Get a structural assembly by entry and assembly ID
GET
/core/chemcomp/{comp_id}
Get a chemical component by CCD ID
GET
/core/drugbank/{comp_id}
Get DrugBank annotations for a chemical component
GET
/core/interface/{entry_id}/{assembly_id}/{interface_id}
Get a pairwise polymeric interface description
GET
/core/entry_groups/{group_id}
Get an aggregated entry group
GET
/core/branched_entity/{entry_id}/{entity_id}
Get a branched entity by entry and entity ID
Jentic AI Readiness Score
This API is usable in Jentic One now. Its AI-readiness score against Jentic's framework shows where it stands today and where improvements would make it even easier for agents to use.
R
RCSB RESTful API
- AI-Aware (B+)68/100
49
Foundational Compliance62
Developer Experience & Jentic Compatibility57
AI-Readiness & Agent Experience94
Agent Usability100
Security100
AI DiscoverabilityPowered by JenticScoring Framework 1.0.0 | Scoring Engine 0.4.0
Show dimension breakdown
49
Foundational Compliance
Base layer of spec validity and structural soundness.
Grade: D+Signals: 4
78%
Lint Results
Aggregated quality score from linter diagnostics, weighted by severity.
100%
Resolution Completeness
Percentage of `$ref` references that resolve successfully.
0%
Specification Validity
Checks whether the API description parses successfully and conforms to its declared specification (e.g., OpenAPI).
17%
Structural Integrity
Structural correctness score based on schema issues using logarithmic dampening.
62
Developer Experience & Jentic Compatibility
Clarity, completeness, and ingestion readiness for developers and tooling.
Grade: B-Signals: 4
23%
Example Density
How richly the API is illustrated with examples.
82%
Example Validity
Percentage of examples that conform to their schemas.
51%
Response Coverage
Percentage of operations with complete response definitions (success, client error, server error).
93%
Tooling Readiness
Health of API ingestion, bundling, and resolution within Jentic pipelines.
57
AI-Readiness & Agent Experience
Semantic breadth, depth, and agent comprehension for AI systems.
Grade: CSignals: 4
76%
Description Coverage
Coverage of descriptions across API elements.
0%
Error Standardization
Coverage of RFC 9457 Problem Details for error responses.
100%
OperationId Quality
Coverage, uniqueness, and casing consistency of operationIds for AI inference.
50%
Summary Coverage
Coverage of summaries across operations/tags/info.
94
Agent Usability
Functional utility, complexity comfort, and AI orchestration readiness.
Grade: A+Signals: 1
94%
Complexity Comfort
Agent comfort level based on API operational and structural complexity.
100
Security
Trust, risk posture, and security compliance.
Grade: A+Signals: 1
100%
Authentication Strength
Average quality of security schemes based on authentication method strength (weakest link for OAuth2).
100
AI Discoverability
Findability, semantic richness, and reasoning readiness.
Grade: A+Signals: 1
100%
Descriptive Richness
Clarity and depth of descriptions across API elements.
Score it yourself
Every API in the directory is allowlisted, so you can re-score it with no key required.
npx @jentic/api-scorecard-cli score <openapi-url>Why Jentic?
What agents get from Jentic-routed access to this vendor.
Setup
The RCSB RESTful API is unauthenticated, so wiring it by hand still leaves you building the base URL resolution, retry, and rate-limit plumbing for entry, entity, and chemical component reads yourself. Through Jentic you install once, import the RCSB RESTful API from the API Directory, and your agent calls it through a consistent execution layer.
Permission scoping
RCSB puts the entry, assembly, and component ids in the URL path (/core/entry/{entry_id}, /core/assembly/{entry_id}/{assembly_id}), so a rule can pin your agent to specific entries or components. This API is read-only, so the agent can only retrieve the published records you allow it to.
Credential isolation
RCSB endpoints are unauthenticated, so there is no credential to store, and Jentic still routes every call through its own execution layer for consistent retry and logging. No token enters the agent's prompt, logs, or context.
Intent-based discovery
Agents search Jentic by intent such as 'get a PDB entry' or 'look up a chemical component', and Jentic returns the matching RCSB operation with its input schema so the agent calls the right endpoint without parsing the RCSB reference.
Related APIs
Alternatives and complements available in the Jentic catalogue.
FAQs
Specific to using RCSB RESTful API through Jentic.
Why is there no official OpenAPI spec for the RCSB RESTful API?
RCSB publishes a Redoc-rendered API doc but not a structured OpenAPI specification. Jentic generates and maintains this spec so that AI agents and developers can call the RCSB RESTful API via structured tooling. It is validated against the live API and kept up to date. Get started with Jentic One, the self-hosted execution layer.
What authentication does the RCSB RESTful API use?
The RCSB RESTful API is fully public and requires no authentication. Jentic still routes calls through its execution layer so agents benefit from consistent rate-limiting, retries, and logging across providers.
Can I retrieve a PDB entry by ID with this API?
Yes. GET /core/entry/{entry_id} returns the structure record for the supplied PDB entry ID, and the related GET /core/assembly/{entry_id}/{assembly_id} endpoint returns the biological assembly detail.
What are the rate limits for the RCSB RESTful API?
RCSB does not publish hard rate limits but advises avoiding sustained high-frequency requests against the public service. Apply client-side caching of entry records and exponential backoff on 429 or 503 responses for batch jobs.
How do I look up a chemical component through Jentic?
Run pip install jentic, then search Jentic for 'look up a chemical component', load the GET /core/chemcomp/{comp_id} schema, and execute it with the CCD ID. Pair with GET /core/drugbank/{comp_id} for DrugBank annotations.
Does the RCSB RESTful API support interface and entity instance lookups?
Yes. GET /core/interface/{entry_id}/{assembly_id}/{interface_id} returns pairwise polymeric interface descriptions and the entity-instance endpoints return descriptions keyed by entry ID and asym ID for polymer, non-polymer, and branched entities.
Can I limit what my agent is allowed to do with the RCSB RESTful API?
Yes. Because you run Jentic One yourself, your own rules decide which RCSB operations and inputs the agent may call. This API is read-only, so an agent can at most retrieve published records, and since RCSB puts identifiers in the URL path (GET /core/entry/{entry_id}, GET /core/assembly/{entry_id}/{assembly_id}, GET /core/chemcomp/{comp_id}), you can pin the agent to specific entries, assemblies, or chemical components. Any operation you do not permit stays out of the agent's reach.
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