Systematic medical reviews and evidence-based healthcare research
Free
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, 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 / org
ArgumentsA call is made on an account: it counts against an allowance and the publisher sees it, which is why this one asks who you are first.
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p95 latency
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call success
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uptime 90d
0
calls last 7d
What it does
Federated protein structure and annotation search across PDB, AlphaFold DB, 3D-Beacons, UniProt and InterPro.
Quickstart
# 1 — install (mcprush login holds a key from your dashboard)
npx mcprush@latest add protein-structures-pdb-alphafold-mcp
# 2 — ask your agent something
> Federated protein structure and annotation search across PDB, AlphaFold DB, 3D-Beacons, UniProt and InterPro.
Protein Structures (PDB/AlphaFold) is free: there is no plan to choose, no cap to set and nothing that can bill you.
Publishernot claimed
PRAll 1 server
protein.caseyjhand.com1 server
1 category
Collected from a public index. Nobody has claimed this account, so nothing here was written by its author — claim it if it is yours.
Installation
Where are you running it?
Every route below installs the same thing and ends at the same approval screen. Nothing here runs on your machine — this server runs on the publisher’s own infrastructure behind our gateway, and what you install is the connection to it.
Claude Codedeclared by this listing
This is a public server: you run it yourself and this marketplace is not in the path. Claude Code registers it in one command.
claude mcp add --transport http protein-structures-pdb-alphafold-mcp https://protein.caseyjhand.com/mcpReconnect, or start a new session, and the tools appear in the model’s tool list.
Free to install, and it runs from its publisher’s own package: no account, no key, no card.
What it writes
One config entry pointing at the gateway. The server itself runs on the publisher’s own infrastructure, so nothing from this listing executes on your machine.
What you approve
7 tools, with what each one reads, writes and reaches shown before you agree — the same list on every route above. Read the tool surface.
Tool surface
What the model actually sees. Descriptions are diffed on every release — see version history.
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 / org
Takes no parameters.
Example callreturns →
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 accession
Takes no parameters.
Example callreturns →
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
Takes no parameters.
Example callreturns →
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 li
Takes no parameters.
Example callreturns →
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 budge
Takes no parameters.
Example callreturns →
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
Takes no parameters.
Example callreturns →
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
Takes no parameters.
Example callreturns →
Freeyour plan
$0 forever
- Every tool, no call limit
- No card, no account needed
- Source published under a licence you can read
- Runs on your machine — nothing of it reaches our gateway
- Nothing to cap, because nothing bills
What counts against your monthly calls
| Tool | Unit | Calls used | Out of the allowance |
|---|
Nothing here is billable. Protein Structures (PDB/AlphaFold) costs nothing to install and nothing to call, at any volume.
Call allowance · this installenforced at the gateway
Monthly allowance, in calls
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Alert at 80% · then the tool returns a normal MCP error
Used this month: $8.42
$16.58 left
—Grade not published
No rule-by-rule report on file for this release
Two independent axes, because powerful and malicious are different questions. The grade is threat only. The capability level is blast radius, and it is never a penalty on the grade — it is priced as one subtract-only term in the score, where you can see it.
This listing is a hosted endpoint: the publisher runs it and we connect to it. The scanner reads packages and source, and neither exists to read here, so there is no grade — not a withheld one, an unmeasured one. What can be checked instead is on Installation: what it asks to reach and what it writes.
Release history
Pinned to 0.5.1 — the install command below asks for that release. A pin is part of an install, so it is kept for this visit and written down when you install.
0.5.1
undated
installedNo release note was published with this version.
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no reviews yet
Reviews are earned
Only accounts with at least 50 real tool calls against this server in the last 90 days can post. Ratings are weighted by how much the reviewer actually uses it, and publishers can reply once per review.
Reviews are earned
Writing one takes an account with at least 50 real tool calls against Protein Structures (PDB/AlphaFold) in the last 90 days. That is the whole gate — there is no other way to post, which is why the counts beside each review are worth reading.
No reviews yet
Nobody has reviewed this listing. The rating on the card is the mean of the reviews written here and nothing else, so there is no rating until somebody writes the first — which takes an account with 50 real tool calls against it.