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RCSB PDB

Searches, inspects, and cross-references Protein Data Bank structures through MCP tools.

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Install RCSB PDB

Pick your client, then add it in one click or paste the config.

STDIOPython
~/Library/Application Support/Claude/claude_desktop_config.json
claude_desktop_config.json
{
  "mcpServers": {
    "rcsb-pdb-2": {
      "command": "uvx",
      "args": [
        "rcsb-mcp"
      ]
    }
  }
}

Settings → Developer → Edit Config, merge this into mcpServers, then fully quit and reopen Claude Desktop.

Automated check passed— started and listed 36 tools correctly (5d ago).

Overview

The RCSB PDB MCP server lets agents search, inspect, and cross-reference Protein Data Bank structures. It uses RCSB Search, Data, and Sequence Coordinates APIs for keyword, attribute, sequence, chemical, shape, motif, entry, entity, and annotation queries. Use it when an agent needs to identify relevant structures, retrieve detailed records, or connect PDB data with UniProt and related references.

Use cases

  • Find protein structures by sequence similarity
  • Search entries by organism, resolution, or release date
  • Resolve biological terms before querying PDB annotations
  • Inspect assemblies, interfaces, ligands, and chains
  • Cross-reference PDB records with UniProt and PubMed

Key features

  • Keyword and structured attribute search
  • Sequence, chemical, shape, and motif searches
  • GO, InterPro, EC, disease, and taxonomy term resolution
  • PDB entity, assembly, interface, and ligand retrieval
  • Live GraphQL data-object schema inspection

Tools36

What RCSB PDB lets your agent do. Expand a tool for its parameters.

Verified live~16.6k tokens of context

Security & health

What it can reach and how reliably it runs — from our own checks, not the maintainer’s claims.

ActiveLast checked 3d ago

Recent health check succeeded.

7/7 checks healthy over the last 46d

What it can do

From the 36 tools this server returned when we ran it; 36 declare their own safety hints.

Runs commands · 2Makes network requests · 36Read-only tools · 34
Unusual tool instructions. 1 tool description contain text aimed at the AI model rather than at you (asks the assistant to hide something from the user). Read the tool descriptions before connecting.
Network at startup2 connections
Files written at startup30

Observed 2026-10-19 in an isolated sandbox. A description of reach, not a security audit.

Supply-chain signal

No high-severity advisories surfaced by our automated scan.

Critical 0High 0Medium 0Low 0

Scanned 13d ago via OSV.dev · rcsb-mcp (PyPI)

Adoption & maintenance

Factual signals from GitHub, npm, and our automated checks — not a rating.

GitHub stars11Stargazers on the source repository.
Last commit12d agoMost recent push to the default branch.
Availability100%Our rolling endpoint + install checks that succeeded.
Install checkPassedOur sandbox started it and listed its tools.
Tools exposed36Callable tools this server registers over MCP.
Directory activity1 viewsConfig copies, upvotes, and views on AllMCPs.

How RCSB PDB works

What RCSB PDB MCP server does

The RCSB PDB MCP server gives MCP clients access to the RCSB Protein Data Bank for structure discovery and record inspection. It supports free-text searches, indexed attribute filters, sequence similarity, chemical descriptors, 3D shape similarity, sequence motifs, and structural motifs. Agents can also resolve biological terms into identifiers from external annotation services before searching related PDB records.

The server covers several levels of structural data. It can retrieve entries, polymer and nonpolymer entities, branched entities, entity instances, assemblies, interfaces, chemical components, entry groups, sequence-cluster groups, UniProt records, PubMed records, and grouping provenance.

How it works

Search operations can begin with searchable metadata or terminology resolution. rcsb_list_pdb_search_attributes exposes available paths, types, and operators for structure or chemical schemas. Specialized tools resolve Gene Ontology, InterPro, Enzyme Commission, MONDO disease, and NCBI Taxonomy terms, returning identifiers and PDB entry counts that can guide a follow-up search.

Search tools support keyword and structured queries, as well as similarity-based discovery. Attribute filters can be combined with a single AND or OR operator, while sequence, chemical, shape, and motif searches address more specialized retrieval tasks. Search responses can be limited or paged, and the available search interface supports sorting, facets, grouping, total counts, and optional inclusion of computed models where applicable.

For inspection, the server connects to the RCSB Data API and accepts identifiers such as 4HHB, 4HHB_1, 4HHB.A, or 4HHB-1. Data lookups accept lists of identifiers, and callers can request curated defaults or provide a GraphQL field selection. rcsb_describe_data_object helps discover valid data paths before requesting custom fields.

Tools and capabilities

The RCSB PDB MCP server includes tools for:

  • Finding structures by text, attributes, sequence, chemical descriptor, 3D shape, sequence motif, or structural motif.
  • Discovering searchable structure and chemical attributes.
  • Resolving GO, InterPro, EC, MONDO, and taxonomy terms into identifiers usable in PDB searches.
  • Retrieving entries, entities, chains, assemblies, interfaces, ligands, glycans, groups, UniProt records, and PubMed records.
  • Inspecting the live Data API schema and selecting verified GraphQL fields.

Limitations and notes

The RCSB PDB MCP server depends on the RCSB APIs and on external services used for terminology resolution, including EBI services and UniProt taxonomy data. Search results identify matching records; detailed information requires a subsequent data lookup. Chemical-component searches use a separate schema and may require chemical-specific attributes and return types.

Nested attributes have different matching semantics depending on whether conditions are supplied together or in separate calls. Sorting is limited to attributes indexed for sorting, and grouping requires polymer-entity results. Requests for all hits are restricted above 10,000 matches, while ordinary pagination uses limits and offsets.

It does not specify installation commands, environment variables, authentication requirements, or a license.

Read the full README View source on GitHub

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Frequently Asked Questions about RCSB PDB

RCSB PDB is an MCP server that connects AI clients to the RCSB Protein Data Bank and related RCSB APIs. Its main tools search structures by text, attributes, sequence, chemistry, shape, and motifs, then retrieve entries, entities, assemblies, interfaces, annotations, UniProt records, and PubMed references.

It identifies the project repository and names Claude Desktop, MCP Inspector, and Cursor as MCP clients that can use it.

Yes, Cursor is named as an MCP client for the RCSB PDB server.

Use the sequence-search capability exposed by the RCSB PDB server, which performs MMseqs2 sequence-similarity searches. Results can be refined through supported search options and then inspected with the server's data retrieval tools.

Yes, it provides tools for retrieving biological assemblies and assembly interfaces. Assembly identifiers use forms such as `4HHB-1`, while interface identifiers use forms such as `1BMV-1.1`.

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