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Nothing to run from here
Protein Structures (PDB/AlphaFold) is installed from its publisher's own source and answers where it runs, so this marketplace is not in the path of a single call. There is no address here to send one to, and a panel that pretended otherwise would be showing you an answer we made up. Install it and call it from your own client — the Installation tab has the entry for each one.
7
tools declared
—
trust score
remote
at its publisher
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calls last 7d
What it does
Federated protein structure and annotation search across PDB, AlphaFold DB, 3D-Beacons, UniProt and InterPro.
Quickstart
# 1 — add it to Claude Code
claude mcp add --scope user --transport http protein-structures-pdb-alphafold-mcp https://protein.caseyjhand.com/mcp
# 2 — ask your agent for something these tools do
# protein_search_structures, protein_get_structure, protein_find_similar and 4 more
Protein Structures (PDB/AlphaFold) costs nothing on mcprush: there is no plan to choose here, no cap to set and nothing mcprush can bill you for.
Publishernot claimed
PCAll 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 and nothing runs on ours: this server answers at its publisher’s own address, and what you install is the connection straight to it.
Claude Codedeclared by this listing
This is a public server: it answers at its publisher’s own address and this marketplace is not in the path. Claude Code registers it in one command; --scope user makes it available in every project. The transport below is http, read from the address; if the publisher says otherwise, swap that one word.
claude mcp add --scope user --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 on mcprush, and it answers at its publisher’s own address: this marketplace is not in the path, so there is no key of ours to hold and no card to add.
What it writes
One config entry pointing straight at the publisher’s own address — this marketplace is not in the path, and 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
| Parameter | Type | Required | Notes |
|---|---|---|---|
| query | string | no | Free-text query (protein name, gene, keyword, PDB title terms). |
| sequence | string | no | One-letter amino-acid sequence; triggers an RCSB mmseqs2 sequence-similarity search. |
| organism | string | no | Filter by source organism scientific name (e.g. "Homo sapiens"). |
| method | string | no | Filter by experimental method (e.g. "X-RAY DIFFRACTION", "ELECTRON MICROSCOPY"). |
| max_resolution | number | no | Maximum resolution in Å (lower is sharper); applies to experimental structures. |
| min_identity | number | no | Minimum sequence identity (0–1) for a sequence search. Default 0. |
| max_evalue | number | no | Maximum E-value for a sequence search. Default 1. |
| content_type | string | no | Which structure universe to search: experimental (PDB), predicted (computed models), or all. |
| facets | array | no | Optional dimensions to summarize as a facet breakdown alongside the hits. Each dimension at most once; repeating one is rejected. |
| limit | integer | no | Maximum hits to return (1–100). |
| start | integer | no | Zero-based result offset. Combine with limit to retrieve later pages. |
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
| Parameter | Type | Required | Notes |
|---|---|---|---|
| ids | array | yes | PDB entry IDs or computed-model IDs such as AF_AFP69905F1 (source experimental), or UniProt accessions (predicted / best_available). |
| source | string | no | Where to fetch: experimental (PDB), predicted (AlphaFold), or best_available (federated pick). |
| include_coords | boolean | no | Inline coordinate-file content (cif). Off by default — URLs are always returned. |
| sections | array | no | Structure IDs to inline coordinates for, from a prior overflow outline. |
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
| Parameter | Type | Required | Notes |
|---|---|---|---|
| by | string | yes | Similarity axis: sequence (mmseqs2) or structure (Foldseek). |
| sequence | string | no | One-letter amino-acid sequence to search from (by:sequence). |
| pdb_id | string | no | PDB entry ID to derive the query from. |
| uniprot | string | no | UniProt accession to derive the query from. |
| ticket_id | string | no | Foldseek ticket ID from a prior by:structure response whose status was "computing". When set, polls that existing job instead of submitting a new search (by:structure only) — pdb_id/uniprot/databases |
| databases | array | no | Foldseek target databases (by:structure). Default pdb100 + afdb50. e.g. afdb-swissprot, BFVD. |
| max_evalue | number | no | Maximum E-value (by:sequence). Default 1. |
| min_identity | number | no | Minimum sequence identity 0–1 (by:sequence). Default 0. |
| limit | integer | no | Maximum hits to return (1–100). |
| start | integer | no | Zero-based result offset (by:sequence 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. mode "structures_with_ligand" returns PDB entries containing a li
| Parameter | Type | Required | Notes |
|---|---|---|---|
| mode | string | yes | Operation: resolve a ligand, find structures containing it, or analyze its binding site. |
| query | string | no | Ligand name or formula (mode find_ligand). |
| comp_id | string | no | Exact chemical component ID (modes structures_with_ligand and binding_site). |
| pdb_id | string | no | PDB entry ID (mode binding_site). |
| limit | integer | no | Maximum results to return (1–100). |
| start | integer | no | Zero-based result offset (mode structures_with_ligand 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, fanned out with a concurrency cap and per-pair partial success — a pair still computing when the budge
| Parameter | Type | Required | Notes |
|---|---|---|---|
| structures | array | yes | The structures to compare, up to the configured batch cap (excess is dropped with a notice). A structure repeated here is compared once. |
| reference | string | no | Align all to the first structure, or compute the full pairwise matrix. |
| method | string | no | Alignment algorithm: tm-align, fatcat-rigid, or fatcat-flexible. |
| timeout_s | integer | no | Poll budget per pair in seconds before returning "computing". Defaults to the server setting. |
| resume | array | no | Resume tickets from a prior call: for each pair whose labels match an entry here, poll the existing UUID instead of submitting a new alignment job. Copy a, b, and uuid verbatim from a prior response's |
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
| Parameter | Type | Required | Notes |
|---|---|---|---|
| group_by | array | yes | 1 dimension for a breakdown, or 2 distinct dimensions for a cross-tab (the first nests the second). Repeating a dimension is rejected. |
| query | string | no | Optional free-text scope (e.g. "kinase"); omit to profile the whole PDB. |
| organism | string | no | Optional source-organism scope. |
| method | string | no | Optional experimental-method scope. |
| max_resolution | number | no | Optional maximum-resolution scope (Å). |
| content_type | string | no | Which structure universe to profile. Default experimental. Computed models carry no experimental metadata, so method and resolution return nothing under "predicted". |
| interval | no | Bin width for a histogram dimension (number) or period for a date histogram (year/month/quarter). | |
| bucket_limit | integer | no | Max buckets per dimension level, not per response. A cross-tab applies the cap separately to the parent dimension and to the nested child inside each parent bucket, so up to bucket_limit × (1 + bucket |
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
| Parameter | Type | Required | Notes |
|---|---|---|---|
| uniprot | string | no | UniProt accession (e.g. P69905). Takes precedence over pdb_id. |
| pdb_id | string | no | PDB entry ID; resolved to a UniProt accession via cross-reference. |
| chain | string | no | Author chain ID (auth_asym_id, e.g. "A") that disambiguates a multi-chain PDB entry to a specific UniProt accession. Case-sensitive — must match the author chain ID exactly (large structures can carry |
| include | string | no | Which annotation classes to fetch: features, domains (InterPro), variants, or all. |
| limit | integer | no | Per-class cap (1–200): features, natural variants, and InterPro domains are each independently truncated to at most this many records. The default keeps a typical annotation set intact while bounding |
Free
$0 forever
- Every tool — any call limit is its publisher’s, not ours
- No card, and mcprush charges nothing for it
- Runs at its publisher’s own address — this marketplace is not in the path
- Nothing to cap, because mcprush bills nothing
What counts against your monthly calls
| Tool | Unit | Calls used | Out of the allowance |
|---|
Nothing here is billable: mcprush charges nothing to install Protein Structures (PDB/AlphaFold) or to call it, 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: —
—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 an address its publisher runs, and you connect to it directly — this marketplace is not in the path. The scanner reads packages and public source, and an address is neither. So there is no grade — not a withheld one, an unmeasured one.
Release history
This is an address its publisher runs: which release it serves is theirs to choose, so there is nothing here to pin. The history below is for reading; the current release on file is 0.5.1.
0.5.1
undated
latestNo release note was published with this version.
—
no reviews yet
Who can review
One review per account, from a signed-in account that does not publish this listing. Nothing else is asked — you can say what you think before you install it. Publishers can reply once per review, and a review can be edited or deleted by whoever wrote it.
Sign in to write one
Any signed-in account that does not publish Protein Structures (PDB/AlphaFold) can review it, once — before installing it or after. A review from an account that has installed it is marked as one.
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