# protein-mcp-server MCP server

Federated protein structure & annotation across experimental (PDB) and predicted (AlphaFold) models.

## Links
- Registry page: https://www.getdrio.com/mcp/io-github-cyanheads-protein-mcp-server
- Repository: https://github.com/cyanheads/protein-mcp-server

## Install
- Command: `npx -y @cyanheads/protein-mcp-server`
- Endpoint: https://protein.caseyjhand.com/mcp
- Auth: Not captured

## Setup notes
- Package: Npm @cyanheads/protein-mcp-server v0.4.0
- Environment variable: MCP_LOG_LEVEL (default info)
- Package: Npm @cyanheads/protein-mcp-server v0.4.0
- Environment variable: MCP_HTTP_HOST (default 127.0.0.1)
- Environment variable: MCP_HTTP_PORT (default 3010)
- Environment variable: MCP_HTTP_ENDPOINT_PATH (default /mcp)
- Environment variable: MCP_AUTH_MODE (default none)
- Environment variable: MCP_LOG_LEVEL (default info)
- Remote endpoint: https://protein.caseyjhand.com/mcp

## Tools
- protein_search_structures (protein-mcp-server: 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, and resolution filters. Returns ranked hits; the experimental page is enriched with title, method, resolution, and organism. Chain hit IDs into protein_get_structure. Optionally returns a facet breakdown (counts by method / organism / release year / …) alongside the hits at no extra call. A facet on a dimension you are already filtering (e.g. the organism facet while organism is set) lists unfiltered alternatives by design — it does not constrain by its own active filter, so you can see sibling values to pivot to. Numeric histogram buckets (resolution, molecular weight) carry explicit rangeFrom/rangeTo bounds so a boundary label is unambiguous. Endpoint: https://protein.caseyjhand.com/mcp
- protein_get_structure (protein-mcp-server: get structure) - Fetch structures with metadata and coordinate-file URLs. source "experimental" takes PDB entry IDs (batched in one call), 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 UniProt accessions (AlphaFold, with pLDDT/PAE confidence); "best_available" takes UniProt accessions and returns the top federated model — the highest-resolution experimental structure if one exists (optimizing resolution, not biological representativeness, so it can return an engineered mutant over the wild-type entry), else the best prediction. Resolves up to the configured batch cap per call with per-ID partial success — missed IDs are listed in failed[]. Set include_coords to inline coordinate content; if that overflows, a section outline is returned — re-call with sections:[ids] to inline specific structures. Endpoint: https://protein.caseyjhand.com/mcp
- protein_find_similar (protein-mcp-server: find similar) - Find structurally or evolutionarily related proteins. by:"sequence" runs an RCSB mmseqs2 sequence-similarity search (synchronous) over a sequence — supplied directly, or pulled from a PDB ID or UniProt accession. by:"structure" runs a Foldseek fold-similarity search (asynchronous) against experimental and predicted databases; if the job is still computing when the poll budget elapses, the response reports status "computing" with a ticket — re-call with ticket_id set to that value to resume the same job instead of resubmitting. Output names the engine and database each hit came from. Endpoint: https://protein.caseyjhand.com/mcp
- protein_track_ligands (protein-mcp-server: 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 for the name, not necessarily an exact name-string match. mode "structures_with_ligand" returns PDB entries containing a ligand (by exact component ID — get the ID from find_ligand first), highest-resolution first, each with its resolution in Å. mode "binding_site" returns the protein residues lining a ligand's pocket in a given structure, with contact distances. Binding sites are experimental-only (computed from deposited coordinates; predicted models carry no bound ligands). Endpoint: https://protein.caseyjhand.com/mcp
- protein_compare_structures (protein-mcp-server: compare structures) - Structurally align multiple structures (up to the configured batch cap) via the RCSB Structural Comparison service (TM-align / jFATCAT). reference:"first" aligns every structure to the first; reference:"all_pairs" computes the full pairwise matrix. Each pair is an independent async alignment job, fanned out with a concurrency cap and per-pair partial success — a pair still computing when the budget elapses returns status "computing" with its job UUID, and a failed pair degrades its row without sinking the others. Re-call with a matching entry in resume[] to poll a computing pair's UUID instead of resubmitting. Returns TM-score, RMSD, and aligned-residue count per pair, plus each structure's modeled-residue count and alignment coverage. TM-score is length-normalized and can shift sharply between structures that differ only by a terminal residue or two — the greedy superposition can settle into a worse local optimum — so read tmScore alongside rmsd, alignedResidues, modeledResidues and coverage, the columns that make such cases diagnosable. Endpoint: https://protein.caseyjhand.com/mcp
- protein_analyze_collection (protein-mcp-server: 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 server-side at RCSB — one call returns compact buckets, no row pull. Pass one group_by dimension for a single breakdown, or two distinct dimensions for a cross-tab (the first nests the second). bucket_limit caps each dimension level separately rather than the response, so a cross-tab returns up to that many nested buckets under each of its capped parent buckets; bucketsReturned reports the realized total. Endpoint: https://protein.caseyjhand.com/mcp
- protein_get_annotations (protein-mcp-server: get annotations) - Sequence and functional annotation for a protein: UniProt features (domains, binding sites, PTMs), natural variants, and InterPro domain/family memberships (Pfam, PROSITE, …) with GO terms. Provide a UniProt accession directly, or a PDB ID — it is resolved to its UniProt accession via the structure's sequence cross-reference. A multi-chain PDB entry can map to several accessions; the default pick is deterministic (lowest author chain ID) and the alternatives are listed in "ambiguity" — pass "chain" to select a specific one. Use "include" to scope which annotation classes are fetched. Every response carries an "attribution" block with the upstream data licenses and citations. Endpoint: https://protein.caseyjhand.com/mcp

## Resources
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## Prompts
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## Metadata
- Owner: io.github.cyanheads
- Version: 0.4.0
- Runtime: Npm
- Transports: STDIO, HTTP
- License: Not captured
- Language: Not captured
- Stars: Not captured
- Updated: Jul 3, 2026
- Source: https://registry.modelcontextprotocol.io