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RCSB PDB MCP server

by rcsb·io.github.rcsb/rcsb-mcp·v0.15.0
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MCP server to search, inspect, and cross-reference RCSB Protein Data Bank structures

A89/100grade A
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Safety scan
A89/100

full report

Adoption
Growing

4 stars69 downloads/wk

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If you have run it, two minutes of your experience saves the next person an afternoon.

RCSB PDB tools (6, 1 write)

write = sends, deletes, buys or posts

Read from the package source without running it. The installed server may list more.

  • _drop_titlewrite action

    `title` — pydantic derives it from the key it sits next to.

  • rcsb_render_report

    Render a structure-search report as a styled, self-contained HTML page.

  • register_data_tools

    Attach the RCSB Data API tools (rcsb_get_* / rcsb_describe_data_object) to a FastMCP server.

  • register_resolver_tools

    Attach the ontology/identifier resolver tools (rcsb_find_*) to a FastMCP server.

  • register_search_tools

    Attach the RCSB Search API tools (rcsb_query_* / rcsb_search_request) to a server.

  • register_seqcoord_tools

    Attach the Sequence Coordinates API tools (rcsb_seqcoord_* / rcsb_describe_seqcoord_object) to a FastMCP server.

Public scan report

scanner v0.1.9 · 2026-09-23 · same rubric, same numbers if you re-run it

no findings
  • Code scan35 source files scanned25/25
  • –Live reliabilityno gateway calls yet and no remote to proben/a
  • –Tool poisoningtools not inspected (local package is not executed); not countedn/a
  • Auth qualitylocal package, no credentials required12/15
  • Maintenancelast push 37 days ago12/15
  • Maintainer identityregistry namespace matches repository owner; GitHub account older than a year9/10
Overall 89/100. Components that don't apply are left out of the denominator. Any critical finding is an F.RubricAppeal a findingJSON

What the publisher says

From the RCSB PDB repository's README, as published. We do not edit it. Read it on GitHub

<!-- mcp-name: io.github.rcsb/rcsb-mcp -->

rcsb-mcp

An MCP server for interrogating Protein Data Bank structures — discover, inspect, and cross-reference — from LLM clients (Claude Desktop, MCP Inspector, Cursor, etc.). It spans three RCSB APIs:

(keyword, attribute, sequence, chemistry, 3D shape, motif).

  • Discover — find structures with the Search API

from the Data API.

  • Inspect — fetch entry / entity / assembly / ligand details and annotations

with the Sequence Coordinates API.

  • Relate — map sequences and positional features across PDB, UniProt, and NCBI

Tools

Search (search.rcsb.org)

The two text tools (rcsbsearchfulltext, rcsbsearchbyattribute) also take groupbyidentity (100/95/90/70/50/30) to return one representative per sequence-identity cluster — i.e. non-redundant results. To search chemical-component attributes, find the path with rcsblistpdbsearchattributes(schema="chemical"), then pass chemical=True to rcsbsearchbyattribute / rcsbsearchfulltext (usually with returntype="moldefinition"). Both catalogs (structure and chemical) are generated from the live metadata schemas by scripts/generatesearchattributes.py.

Shortened. The full README is on GitHub.

Nothing above is checked by us. What we check is on the safety report.

Install directly

claude mcp add rcsb-mcp -- uvx rcsb-mcp
Add to Cursor

RCSB PDB: common questions

Is RCSB PDB MCP server safe?
Yes, by our scan: it is graded A (89/100). Read the RCSB PDB safety report
How do I install RCSB PDB?
It runs on your machine. Copy the Claude Code, Claude Desktop or Cursor config from the install section.
Does RCSB PDB need an API key?
Not as far as the registry entry and our scan can tell: no credentials are declared or required.
Is RCSB PDB maintained?
The last commit was 37 days ago (2026-08-17). The latest release is v0.15.0.
What can I use instead of RCSB PDB?
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