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RCSB PDB MCP — experimentally determined macromolecular structures.
About
RCSB PDB MCP — experimentally determined macromolecular structures.
Remote endpoints: streamable-http: https://gateway.pipeworx.io/rcsb-pdb/mcp
Security Report
10.0
Low Risk10.0Low RiskValid MCP server (1 strong, 0 medium validity signals). No known CVEs in dependencies. Imported from the Official MCP Registry. Trust signals: trusted author (1052/1055 approved). 1 finding(s) downgraded by scanner intelligence.
36 tools verified · Open access · 1 issue found
Security scores are indicators to help you make informed decisions, not guarantees. Always review permissions before connecting any MCP server.
Permissions Required
This plugin requests these system permissions. Most are normal for its category.
How to Connect
Remote Plugin
No local installation needed. Your AI client connects to the remote endpoint directly.
Add this to your MCP configuration to connect:
{
"mcpServers": {
"io-github-pipeworx-io-rcsb-pdb": {
"url": "https://gateway.pipeworx.io/rcsb-pdb/mcp"
}
}
}Documentation
View on GitHubFrom the project's GitHub README.
mcp-rcsb-pdb
RCSB PDB MCP — experimentally determined macromolecular structures.
Part of Pipeworx — an MCP gateway connecting AI agents to 965+ live data sources.
Tools
| Tool | Description |
|---|---|
search | "Find protein structure of [target]" / "search PDB for [protein]" / "is there a crystal structure of [X]" / "[disease target] structures" / "CRISPR / kinase / GPCR structures" — text search the RCSB PDB (the global archive of experimentally-determined 3D protein/RNA/DNA structures). Returns matching PDB IDs you can pass to structure or summary. Use for structural biology, drug design, protein characterization. |
structure | "PDB entry [1abc] details" / "fetch protein structure [pdb_id]" / "metadata for [PDB ID]" — full PDB entry record by ID (e.g. "1abc", "7BV2"). Returns experimental method (X-ray / cryo-EM / NMR), resolution, authors, deposition date, organism, ligands, related entities. Use after search to inspect a specific structure. |
polymer_entity | "Chain [N] of PDB [ID]" / "sequence of chain in [pdb_id]" — fetch the polymer-entity (protein/DNA/RNA chain) metadata for a specific PDB entry. Returns sequence, source organism, UniProt cross-references, GO annotations. Use to drill into one chain of a multi-chain structure. |
ligand | "Ligand / cofactor / drug bound to [pdb_id]" / "small molecule in [PDB entry]" — fetch a non-polymer ligand record (small molecule, cofactor, ion, or bound drug) for a PDB entry. Use to inspect what's bound in a co-crystal structure — common in drug discovery / SBDD. |
assembly | "Biological assembly of [pdb_id]" / "functional oligomer for [PDB entry]" — fetch a biological assembly record (the functional oligomeric unit, which often differs from the crystallographic asymmetric unit). Use when you need the actual functional form of a protein (dimer / tetramer / etc.) rather than the crystal contents. |
summary | Lightweight lookup for a PDB entry by 4-char ID: tries the RCSB UniProt endpoint first, falls back to the core entry record. Returns title, experimental method, resolution, and deposition date without the full polymer/ligand detail of structure. |
Quick Start
Add to your MCP client (Claude Desktop, Cursor, Windsurf, etc.):
{
"mcpServers": {
"rcsb-pdb": {
"url": "https://gateway.pipeworx.io/rcsb-pdb/mcp"
}
}
}
Or connect to the full Pipeworx gateway for access to all 965+ data sources:
{
"mcpServers": {
"pipeworx": {
"url": "https://gateway.pipeworx.io/mcp"
}
}
}
Using with ask_pipeworx
Instead of calling tools directly, you can ask questions in plain English:
ask_pipeworx({ question: "your question about Rcsb Pdb data" })
The gateway picks the right tool and fills the arguments automatically.
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License
MIT
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