protein-mcp-server

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

CommunityOnlineNo sign-inGlobalFreeRead-only

What it can do

  • 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,
  • Protein Get Structure: Fetch structures with metadata and coordinate-file URLs. source "experimental" takes PDB entry IDs (batched in one call); "predicted" takes UniProt accessions (AlphaFold, with p
  • Protein 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 f

What data it sees

Do you need an account

No: the server works without sign-in

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

How to connect

How to connect protein-mcp-server to Claude

The server address to paste into Claude settings:

https://protein-mcp-server--cyanheads.run.tools

  1. Open Claude (claude.ai or the desktop app).
  2. Go to Settings → Connectors.
  3. Click Add custom connector.
  4. Paste the server address copied below into Remote MCP server URL and click Add.
  5. In a chat, click + → Connectors and switch the new connector on.

Custom connectors are available on Free, Pro, Max, Team and Enterprise plans (Free is limited to one). On Team and Enterprise an organization Owner adds the connector first under Organization settings → Connectors.

Authorization

After you click Add, a sign-in window for the service opens. Sign in with your own account and approve access. Claude never sees your password.

How to connect protein-mcp-server to ChatGPT

The server address to paste into ChatGPT settings:

https://protein-mcp-server--cyanheads.run.tools

  1. Open ChatGPT in a browser (chatgpt.com). A Plus, Pro, Business, Enterprise or Edu plan is required.
  2. Turn on developer mode once: Settings → Apps → Advanced settings → Developer mode.
  3. Open Settings → Connectors and click Create.
  4. Fill in the form: Name (anything), Description (one line about what the service does), MCP server URL (copy it below).
  5. Under Authentication choose OAuth if the service requires sign-in, otherwise None. Click Create.
  6. In a new chat open + → Apps/Connectors and enable the connector.

OpenAI has renamed this section before (Connectors → Apps/Plugins). If the label differs, search settings for "developer mode". On Business/Enterprise workspaces an admin must allow custom connectors first.

Authorization

On first use ChatGPT opens the service's sign-in window. Sign in and approve access.

How to connect protein-mcp-server to Cursor

The server address to paste into Cursor settings:

https://protein-mcp-server--cyanheads.run.tools

Fastest: click Open in Cursor below and confirm the prompt.

Manually:

  1. In Cursor open Settings → Cursor Settings → MCP and click Add new global MCP server.
  2. Paste the JSON copied below into ~/.cursor/mcp.json (per project: .cursor/mcp.json in the repo root).
  3. Save the file. The server appears in the MCP list; authorize it there if asked.

Authorization

If the service needs sign-in, an authorize button appears next to the server in the MCP list.

Server tool list (7)

Raw names from tools/list. Only developers need these.

protein_search_structuresSearch 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.
protein_get_structureFetch structures with metadata and coordinate-file URLs. source "experimental" takes PDB entry IDs (batched in one call); "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.
protein_find_similarFind 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.
protein_track_ligandsLigand 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).
protein_compare_structuresStructurally 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. 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 and alignedResidues, the columns that make such cases diagnosable.
protein_analyze_collectionProfile 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 for a cross-tab (the first nests the second).
protein_get_annotationsSequence 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.