Koskamo

RCSB PDB MCP

An MCP server that allows LLM clients to search, inspect, and cross-reference Protein Data Bank structures. It integrates three RCSB APIs: the Search API for finding structures by keyword, attribute, sequence, chemistry, or 3D shape; the Data API for fetching entry, entity, assembly, and ligand details; and the Sequence Coordinates API for mapping sequences across PDB, UniProt, and NCBI.

Package and access

Local package with source-attributed installation metadata. Koskamo does not execute packages during review.

RCSB PDB MCP logo, by RCSBCommunity listingLocal stdioSource reviewed; not executedPublished by RCSB
Vendor documentation

What you can do with it

  • Search PDB structures using keywords, attributes, or sequence similarity
  • Inspect detailed annotations for entries, entities, assemblies, and ligands
  • Map sequences and positional features across PDB, UniProt, and NCBI
  • Resolve molecular functions to Gene Ontology ids or domains to InterPro ids

Source and maintenance

Community listingRegistry 0.23.0
mcp-registry: io.github.rcsb/rcsb-mcp@0.23.0Source repositoryProject website
Maintenance checked

Packages and installation

Source-provided package data. Koskamo has not executed or live-probed this package.

rcsb-mcp 0.23.0

pypiuvx
rcsb-mcp package definition
{
  "version": "0.23.0",
  "transport": "stdio",
  "identifier": "rcsb-mcp",
  "runtimeHint": "uvx",
  "registryType": "pypi",
  "registryBaseUrl": "https://pypi.org"
}

Tools

Reported by the attributed source; not independently observed by Koskamo.

No tool definitions available.

Connect from your client

Each snippet configures the same source-provided package; replace placeholders before use.

This server is operated by the named third party. Listing and endpoint checks are not an endorsement or a security audit. Review the operator's permissions, terms, and data handling before connecting. How listings are checked and corrected.

Cursor

Merge this local stdio configuration, replace every placeholder environment value, and restart Cursor. Koskamo has not executed this package.
Cursor configuration
{
  "mcpServers": {
    "rcsb-pdb-mcp": {
      "command": "uvx",
      "args": [
        "rcsb-mcp==0.23.0"
      ]
    }
  }
}

Cline

Merge this local stdio configuration, replace every placeholder environment value, and restart Cline. Koskamo has not executed this package.
Cline configuration
{
  "mcpServers": {
    "rcsb-pdb-mcp": {
      "command": "uvx",
      "args": [
        "rcsb-mcp==0.23.0"
      ]
    }
  }
}

VS Code

Merge this local stdio configuration, replace every placeholder environment value, and restart VS Code. Koskamo has not executed this package.
VS Code configuration
{
  "servers": {
    "rcsb-pdb-mcp": {
      "type": "stdio",
      "command": "uvx",
      "args": [
        "rcsb-mcp==0.23.0"
      ]
    }
  }
}

Claude Desktop

Merge this local stdio configuration, replace every placeholder environment value, and restart Claude Desktop. Koskamo has not executed this package.
Claude Desktop configuration
{
  "mcpServers": {
    "rcsb-pdb-mcp": {
      "command": "uvx",
      "args": [
        "rcsb-mcp==0.23.0"
      ]
    }
  }
}

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