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find-cocrystal

station__rcsb-org__find-cocrystal external (needs EXECUTION_BACKEND_URL) rcsb-org pv-adjacent Constructa Configa

Find PDB entries containing a given small-molecule ligand (by name or 3-letter chem component code). Use this to discover receptor/ligand cocrystals for mechanism-of-action visualization.

Taxonomy

Linnaean classification joined from the algovigilance taxonomy index via the parent config's rank.

Rank	Value
domain	`Substrata`
kingdom	`Constructa`
phylum	`Configa`
class	`station-config`
order	`rcsb_pdb`
family	`mcp-tool-config`

Characteristics:

substrate: config
domain: pv
lifecycle: continuous
authority: read
compounding: producer
io: agent-request → tool-response

Input schema

ligand stringrequired — Ligand name (e.g., 'caffeine') or 3-letter chem component ID (e.g., 'CFF')
limit integer — Maximum entries to return (default 10, max 25)

Example call

POST /api/mcp
Content-Type: application/json

{
  "jsonrpc": "2.0",
  "id": 1,
  "method": "tools/call",
  "params": {
    "name": "station__rcsb-org__find-cocrystal",
    "arguments": {
      "ligand": ""
    }
  }
}

How to invoke from a client

From any MCP-aware client, add https://algovigilance.com/api/mcp as an MCP server, then call this tool by name. From a raw HTTP client, send the JSON-RPC body above to /api/mcp.

Agent-friendly formats

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All tools (3059 live)
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