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Structurally Superposed Clusters of PDB Chains for a Protein (PDBe-KB)

pdbekbgraph/superposition

For one UniProt accession, the segments of the protein that PDBe-KB has superposed and, per segment, the clusters of PDB chains that share a conformation, each chain with its PDB id, chain ids, entity and whether it is the cluster's representative. Typically 50 to 170 KB. PDBe-KB data (CC BY 4.0), passed through unmodified and served by Eden Engine; not an official PDBe or EMBL-EBI product.

activeper callv1

Price

$0.0026 per call

You pay the price shown. If a call turns out to cost more than its quote, you pay the actual price, capped at twice the quote. No monthly minimum. Top-ups start at $0.50.

Data source

Protein Data Bank in Europe (PDBe), EMBL-EBI

Data from PDBe-KB, the knowledge base of the Protein Data Bank in Europe (EMBL-EBI), published under CC BY 4.0 (https://creativecommons.org/licenses/by/4.0/); cite PDBe-KB per https://www.ebi.ac.uk/pdbe/pdbe-kb/. Served by Eden Engine; not an official PDBe or EMBL-EBI product.

Use it

Five steps: search, inspect, learn, run, settle. No per-tool setup; your agent reaches this tool through the meta-tools it already has.

Connect once and your AI can find and run this tool, and any other it needs.

Install itCreate an account
agent
// 1. search: find the tool
omnial_search({ query: "what you need" })

// 2. inspect: price and input schema
omnial_inspect({ tool: "pdbekbgraph/superposition" })

// 3. learn: read the usage guide at runtime
omnial_learn({ tool: "pdbekbgraph/superposition" })

// 4. run: price the exact call first, then run it
omnial_execute({ tool: "pdbekbgraph/superposition", input: { /* see input_schema */ }, dry_run: true })
omnial_execute({ tool: "pdbekbgraph/superposition", input: { /* ... */ } })

// 5. settle: the call is charged when it finishes, nothing to do

Not connected yet? Point your MCP client at https://mcp.eden-engine.com/mcp, then copy a config for your client.

Pricing

Every charge this tool can incur.

ChargePrice
Per call
$0.0026
Updated
Oct 21, 2026

Input and output schemas

Input schema
input_schema.json
{
  "type": "object",
  "required": [
    "accession"
  ],
  "properties": {
    "accession": {
      "type": "string",
      "pattern": "^[A-Za-z0-9]{6,10}$",
      "description": "UniProt accession of the protein, for example P00533 (human EGFR) or P0DTC2 (SARS-CoV-2 spike)."
    }
  },
  "additionalProperties": false
}
Output schema
output_schema.json
{
  "type": "object",
  "description": "Keyed by the UniProt accession; the value is a list of segments, each with `segment_start`, `segment_end` and `clusters` (lists of chains with `pdb_id`, `auth_asym_id`, `struct_asym_id`, `entity_id`, `is_representative`).",
  "additionalProperties": true
}