Protein MCP Server

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How to connect

Add it to any MCP client that supports remote servers.

{
  "mcpServers": {
    "protein-mcp-server": {
      "type": "http",
      "url": "https://protein.caseyjhand.com/mcp"
    }
  }
}

7 tools

• protein_search_structures

  Search experimental (PDB) and predicted (computed-model) protein structures by free text, protein sequence (triggers an mmseqs2 similarity search), and/or organism, method, resolution, and bound-ligand filters. Returns ranked hits; the experimental page is enriched with title…

• protein_get_structure

  Fetch structures with metadata and coordinate-file URLs. source "experimental" takes PDB entry IDs, and also resolves the computed-model IDs protein_search_structures returns (AF_*/MA_*), which come back marked source "predicted" with their modelling provider; "predicted" takes…

• protein_find_similar

  Find structurally or evolutionarily related proteins. by:"sequence" runs an RCSB mmseqs2 sequence-similarity search (synchronous; experimental PDB entries only — protein_search_structures with a sequence also reaches computed models) over a sequence — supplied directly, taken…

• protein_track_ligands

  Ligand discovery and binding-site analysis across the PDB. mode "find_ligand" resolves a name or formula to chemical component IDs with metadata (formula, weight, SMILES), ranked by deposition frequency — most-deposited component first, so the top hit is the most common match…

• protein_compare_structures

  Structurally align multiple structures (up to the configured batch cap; structures past it are returned in ignored) via the RCSB Structural Comparison service (TM-align / jFATCAT). reference:"first" aligns every structure to the first; reference:"all_pairs" computes the full…

• protein_analyze_collection

  Profile the PDB into distributions and trends over an optional scoping query: counts by method, organism, or polymer composition; resolution and molecular-weight histograms; release-year timelines; and multidimensional cross-tabs (e.g. method × release_year). Aggregation runs at…

• protein_get_annotations

  Sequence and functional annotation for a protein: UniProt positional features (domains, binding and active sites, PTMs including cross-links and lipidation, topology, DNA binding, processing products such as chains and signal peptides, mutagenesis), natural variants, and…

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