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RCSB PDB MCP server

by rcsb·io.github.rcsb/rcsb-mcp·v0.23.0·12 stars
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MCP server to search, inspect, and cross-reference RCSB Protein Data Bank structures

A94/100grade A
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Safety scan
A94/100

full report

Adoption
Growing

12 stars127 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 v0.1.10 · 2026-11-03 · same rubric, same numbers if you re-run it

no findings
  • Code scan81 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 11 days ago15/15
  • Maintainer identityregistry namespace matches repository owner; GitHub account older than a year9/10
Overall 94/100. Components that don't apply are left out of the denominator. Any critical finding is an F.RubricAppeal a findingJSON

How RCSB PDB compares

Against every graded Finance MCP server, from our own scans and uptime checks. Updated after each scan run.

Safety score
94/100
higher than 96% of 1,765 Finance servers
Tools
6
the typical Finance server has 9
Tools that change things
17%
typical: 0%. Fewer write tools means less an agent can break
GitHub stars
12
more than 90% of 957 Finance servers
Downloads a week
127
more than 67% of 505 Finance servers with a package

What its tools let an agent do: 1 read · 4 create · 1 change

Release history: 4 versions in the registry since 2026-08-17, latest 2026-10-23, typically one every 11 days.

Install RCSB PDB in Claude Code, Cursor or VS Code

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

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.

RCSB PDB: common questions

Is RCSB PDB MCP server safe?
Yes, by our scan: it is graded A (94/100). Read the RCSB PDB safety report
How do I install RCSB PDB?
It runs on your machine. Copy the Claude Code, Cursor, VS Code or Claude Desktop 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 23 days ago (2026-10-23). The latest release is v0.23.0.
What can I use instead of RCSB PDB?
Servers from other publishers that do the same job: BankMCP™ MCP server, Beancount.io MCP server and AlgoVault — Crypto Quant Trade Calls MCP server.
How does RCSB PDB compare with other Finance MCP servers?
safety score 94/100 (higher than 96% of 1,765 Finance servers); tools 6 (the typical Finance server has 9); tools that change things 17% (typical: 0%. Fewer write tools means less an agent can break). Full comparison.

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