How do I connect Protein MCP Server to Claude?

The listing records `bunx @cyanheads/protein-mcp-server@latest` as its setup step. Run it, then follow the repository's instructions for the client configuration; the listing names Claude Desktop, Cursor, VS Code as compatible clients.

Is Protein MCP Server free?

The listed licence is Apache-2.0. Check the upstream terms for permitted use and commercial requirements; a public repository does not by itself mean the software is free or open source. Connected APIs and hosted services may have separate charges.

What can Protein MCP Server do?

Protein MCP Server documents 7 tools to the agent, including protein_analyze_collection, protein_compare_structures, protein_find_similar. The descriptions above come from project documentation. A live handshake does not test individual tool behavior.

Protein MCP Server

Unclaimed

by cyanheads

Federated protein structure & annotation across experimental (PDB) and predicted (AlphaFold) models via MCP. STDIO or Streamable HTTP.

Install

$bunx @cyanheads/protein-mcp-server@latest

Set up this server

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This server needs project-specific setup. Follow the project instructions; no reusable public launch command is available yet.

Project instructions

bioinformaticsmcpmcp-serverpdbprotein-structurecyanheadsai-agentalphafoldbundrug-discovery

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7 of 7 tools

Documented tools (7)

From project documentation. A server handshake does not verify each tool’s description or behavior.

protein_analyze_collection

Profile the PDB into distributions and trends with server-side facets — counts, histograms, timelines, and cross-tabs.

protein_compare_structures

Structurally align multiple structures (TM-align / jFATCAT) to a reference or as a full pairwise matrix.

protein_find_similar

Find sequence homologs (RCSB mmseqs2) or fold homologs (Foldseek) from a sequence, PDB ID, or UniProt accession.

protein_get_annotations

Fetch UniProt features and natural variants plus InterPro domain/family memberships with GO terms.

protein_get_structure

Fetch metadata and coordinate-file URLs by ID — experimental (PDB), predicted (AlphaFold), or best-available — with batch partial success and optional coordinate inlining.

protein_search_structures

Search experimental and predicted structures by free text, sequence, or organism/method/resolution filters, with optional facet breakdowns.

protein_track_ligands

Resolve ligand names/formulas to component IDs, find structures containing a ligand, or map binding-site residues.

Tool change history

Compared across complete checks of the same configuration. Tools were listed, not invoked. Input-schema changes are not measured here.

No complete tool checks yet.

FAQ

Questions about Protein MCP Server

How do I connect Protein MCP Server to Claude?: The listing records `bunx @cyanheads/protein-mcp-server@latest` as its setup step. Run it, then follow the repository's instructions for the client configuration; the listing names Claude Desktop, Cursor, VS Code as compatible clients.
Is Protein MCP Server free?: The listed licence is Apache-2.0. Check the upstream terms for permitted use and commercial requirements; a public repository does not by itself mean the software is free or open source. Connected APIs and hosted services may have separate charges.
What can Protein MCP Server do?: Protein MCP Server documents 7 tools to the agent, including protein_analyze_collection, protein_compare_structures, protein_find_similar. The descriptions above come from project documentation. A live handshake does not test individual tool behavior.