PDB Structure Search: Find Protein Data Bank Entries by Keyword (RCSB PDB)

rcsbsearch/search-pdb-structures

Searches the RCSB Protein Data Bank by plain-text keyword (a molecule name, gene, organism, disease or any annotation term) and returns the matching entry ids, best first, each with a relevance score, plus the total number of matching entries. Page through results with start and rows. The search returns identifiers and scores only; details such as title or resolution need a separate lookup by PDB id. Several words must all match; separate alternatives with | and put - before a word to exclude it. A search with no hits returns no body, which arrives as a failed PROVIDER_ERROR run rather than an empty list. RCSB PDB data, passed through unmodified and served by Eden Engine; not an official RCSB PDB 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 $5.

Data source

RCSB Protein Data Bank

Data from the RCSB Protein Data Bank (RCSB PDB, rcsb.org); PDB archive data is CC0 1.0 per rcsb.org/pages/usage-policy. Credit to the original authors of the PDB structure data is encouraged. Served by Eden Engine; not an official RCSB PDB 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.

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agent

// 1. search: find the tool
omnial_search({ query: "what you need" })

// 2. inspect: price and input schema
omnial_inspect({ tool: "rcsbsearch/search-pdb-structures" })

// 3. learn: read the usage guide at runtime
omnial_learn({ tool: "rcsbsearch/search-pdb-structures" })

// 4. run: price the exact call first, then run it
omnial_execute({ tool: "rcsbsearch/search-pdb-structures", input: { /* see input_schema */ }, dry_run: true })
omnial_execute({ tool: "rcsbsearch/search-pdb-structures", 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.

Charge	Price
Per call	$0.0026

Updated: Oct 20, 2026

Input and output schemas

Input schema

input_schema.json

{
  "type": "object",
  "required": [
    "q"
  ],
  "properties": {
    "q": {
      "type": "string",
      "pattern": "^[A-Za-z0-9][A-Za-z0-9 ._,+|()/:-]{0,199}$",
      "description": "The search text, 1 to 200 characters, for example insulin or thymidine kinase. Letters, digits, spaces and . _ , + | ( ) / : - are allowed; double quotes are not. Words are AND-ed by default (all must match), so interferon response factor needs all three; use | between words to match either, for example insulin | glucagon, and put - before a word to exclude it."
    },
    "rows": {
      "type": "integer",
      "default": 10,
      "maximum": 100,
      "minimum": 1,
      "description": "How many hits to return, 1 to 100. Defaults to 10."
    },
    "start": {
      "type": "integer",
      "default": 0,
      "maximum": 9999,
      "minimum": 0,
      "description": "Zero-based index of the first hit to return, 0 to 9999. RCSB documents a ceiling on how deep a search can be paged, so very deep pages may be refused."
    }
  },
  "additionalProperties": false
}

Output schema

output_schema.json

{
  "type": "object",
  "required": [
    "result_type",
    "total_count"
  ],
  "properties": {
    "query_id": {
      "type": "string",
      "description": "RCSB's id for this query."
    },
    "result_set": {
      "type": "array",
      "items": {
        "type": "object",
        "required": [
          "identifier",
          "score"
        ],
        "properties": {
          "score": {
            "type": "number",
            "description": "Relevance score, 1.0 for the best match and lower below it."
          },
          "identifier": {
            "type": "string",
            "description": "The PDB entry id, for example 1BOM."
          }
        },
        "additionalProperties": true
      },
      "description": "This page of hits, best match first."
    },
    "result_type": {
      "type": "string",
      "description": "The kind of identifier returned: entry."
    },
    "total_count": {
      "type": "integer",
      "description": "How many entries match in all, not just on this page."
    }
  },
  "description": "The RCSB Search API response: the total number of matching entries and one page of ranked entry ids. A search with no hits is answered by RCSB with HTTP 204 and no body.",
  "additionalProperties": true
}