Protein MCP Server

Install

Works with Claude Code, Codex, VS Code, Cursor, Windsurf, Claude Desktop. Read the repository before you give any tool access to your data.

npx agentmarket install connector/cyanheads-protein-mcp-server

About

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Permissions

What this server can do and what it asks for, from its tool list and install config. Checked Oct 25, 2026.

Tools

7 read · 0 write · 0 deleteRead-only

Secrets

None asked for

Install scripts

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Runs as

Node.js package

Tools (7)

Read from the source code; the running server may differ. Descriptions are the server’s own words; hidden characters are shown as [U+…].

• protein_analyze_collectionprotein-mcp-server: analyze collectionread-only

  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 RCSB, so the response carries compact counts per bucket rather than the matching entries. 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 …

• protein_compare_structuresprotein-mcp-server: compare structuresread-only

  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 with 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; a resumed pair r…

• protein_find_similarprotein-mcp-server: find similarread-only

  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, and a complete response carries the same ticket so a finished job c…

• protein_get_annotationsprotein-mcp-server: get annotationsread-only

  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 res…

• protein_get_structureprotein-mcp-server: get structureread-only

  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 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)…

• protein_search_structuresprotein-mcp-server: search structuresread-only

  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 in the same response. A facet on a dimension you are already filtering (e.g. the organism facet while organism is set) lists unfiltered alternatives by des…

• protein_track_ligandsprotein-mcp-server: track ligandsread-only

  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. The ranking covers a bounded candidate pool; totalCount and candidatesConsidered report how many components matched and how many were ranked. mode "structures_with_ligand" returns PDB entries containing a ligand (by exact component ID — get the ID from find_ligand …

Signals

Stars

6

Forks

1

Open issues

1

Last commit

Oct 17, 2026 (11 days ago)

Last release

Oct 16, 2026 (12 days ago)

From GitHub (fetched Oct 24, 2026).

Details

Registry name

io.github.cyanheads/protein-mcp-server

Version

1.0.3

Auth

No auth

Packages

npm protein-mcp-servernpm protein-mcp-server

License

Apache-2.0

Repository

github.com/cyanheads/protein-mcp-server

First seen

Oct 24, 2026

Last checked

Oct 24, 2026

Source

Official MCP Registrygithub-graphql