`search`

Pack: rcsb-pdb · Connect: https://pipeworx.io/mcp (see Connect below for a single-pack URL)

No MCP client? Call it directly: GET https://gateway.pipeworx.io/v1/tools/search for the schema, then POST the same URL with its arguments for the data.

“Find protein structure of [target]” / “search PDB for [protein]” / “is there a crystal structure of [X]” / “[disease target] structures” / “CRISPR / kinase / GPCR structures” — text search the RCSB PDB (the global archive of experimentally-determined 3D protein/RNA/DNA structures). Returns matching PDB IDs you can pass to structure or summary. Use for structural biology, drug design, protein characterization.

Parameters

Name	Type	Required	Description
`query`	string	yes	Free-text, e.g. “CRISPR Cas9”.
`return_type`	string	no	entry (default) \| polymer_entity \| non_polymer_entity \| assembly
`limit`	number	no	1-1000 (default 25).

Example call

Arguments

{
  "query": "CRISPR Cas9"
}

curl

curl -X POST https://gateway.pipeworx.io/rcsb-pdb/mcp \
  -H 'Content-Type: application/json' \
  -d '{"jsonrpc":"2.0","id":1,"method":"tools/call","params":{"name":"search","arguments":{"query":"CRISPR Cas9"}}}'

TypeScript (@pipeworx/sdk)

import { Pipeworx } from '@pipeworx/sdk';
const pipeworx = new Pipeworx();

const result = await pipeworx.call('search', {
  "query": "CRISPR Cas9"
});

More examples

{
  "query": "COVID-19 spike protein",
  "return_type": "polymer_entity",
  "limit": 10
}

Response shape

Field	Type	Description
`query_id`	string
`result_type`	string
`total_count`	number
`result_set`	array

Full JSON Schema

{
  "type": "object",
  "properties": {
    "query_id": {
      "type": "string"
    },
    "result_type": {
      "type": "string"
    },
    "total_count": {
      "type": "number"
    },
    "result_set": {
      "type": "array",
      "items": {
        "type": "object",
        "properties": {
          "identifier": {
            "type": "string"
          },
          "score": {
            "type": "number"
          }
        }
      }
    }
  },
  "description": "Search results from RCSB PDB text search"
}

Connect

Add this to your MCP client config — every tool in the catalog, including this one — or use one-click install buttons:

{
  "mcpServers": {
    "pipeworx": {
      "url": "https://pipeworx.io/mcp"
    }
  }
}

Connect to just the rcsb-pdb pack

{
  "mcpServers": {
    "rcsb-pdb": {
      "url": "https://gateway.pipeworx.io/rcsb-pdb/mcp"
    }
  }
}

See Getting Started for client-specific install steps.

search