How to connect
Same URL, five paste targets. Ready surface · Auth required. Not a safe-to-install badge. Handshake this URL
Paste into Settings → MCP or .cursor/mcp.json.
{
"mcpServers": {
"cyanheads-protein-mcp-server": {
"url": "https://protein-mcp-server--cyanheads.run.tools"
}
}
}
Paste into .vscode/mcp.json.
{
"mcpServers": {
"cyanheads-protein-mcp-server": {
"url": "https://protein-mcp-server--cyanheads.run.tools"
}
}
}
Settings → Connectors → Add → Custom → Web. Paste the URL. Enable in a new chat.
Claude → Settings → Connectors → Add → Custom → Web
Name: protein-mcp-server
URL: https://protein-mcp-server--cyanheads.run.tools
OAuth only if this server requires it.
Save, start a new chat, enable the connector.
Developer mode custom connector. ChatGPT cannot reach localhost.
Settings → Apps & Connectors → Advanced → Developer mode ON
Create custom connector
Name: protein-mcp-server
MCP server URL: https://protein-mcp-server--cyanheads.run.tools
Auth: none unless the server requires OAuth
New chat → + → Developer mode → enable the connector
Register the HTTPS URL, then claude mcp list.
claude mcp add --transport http cyanheads-protein-mcp-server \
https://protein-mcp-server--cyanheads.run.tools
Pass on session/new as mcpServers when the agent advertised HTTP MCP.
[
{
"type": "http",
"name": "cyanheads-protein-mcp-server",
"url": "https://protein-mcp-server--cyanheads.run.tools"
}
]
Paste into a README or docs site. The widget loads snippets from Influzer — still not a SAFE badge.
Same handshake clock as this listing (overlay / warm / seed; live tools/list only if that is missing). Indigo is live_ok, amber is auth_required, gray is unreachable. Not a SAFE badge. Stdio listings have no badge.
[](https://www.influzer.ai/mcp/probe?url=https%3A%2F%2Fprotein-mcp-server--cyanheads.run.tools)
<div data-influzer-install="cyanheads-protein-mcp-server"></div>
<script async src="https://www.influzer.ai/embed/install.js"></script>
https://www.influzer.ai/embed/mcp/cyanheads-protein-mcp-server.md
JSON: https://www.influzer.ai/api/v1/install/cyanheads-protein-mcp-server
Recipes using this server
No published recipes yet for this server.
Listing quality
Observable facts from our catalog and daily probe — not a safe-to-install badge.
- Surface
- Ready surface
- Auth gate
- Auth gate
- Tools source
- tools/list (live)
Observable catalog + probe facts — not a safe-to-install badge. How we verify.
Verification summary
Stored signals only. Not a safety score.
- Verification grade
- A (85)
- Last verified
- Status
- Auth required
- Response time
- 0 ms
- Auth
- Auth gate
- Transport
- http, HTTPS
- Tools indexed
- 7
- 30-day uptime
- 100% of 6 samples over 6 days
Probe history
- · auth_required · 0 ms
- · auth_required · 0 ms
- · auth_required · 0 ms
- · auth_required · 0 ms
- · auth_required · 0 ms
Tools
(7)-
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 alread
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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
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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 s
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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 wit
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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 s
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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).
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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 "cha
Tool source: tools/list (live) · last probed 2026-11-04