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get-binding-site

station__rcsb-org__get-binding-site external (needs EXECUTION_BACKEND_URL) rcsb-org pv-adjacent Constructa Configa

Compute the binding pocket for a ligand in a PDB entry: all protein residues with any atom within a distance cutoff (default 5 Å) of any ligand atom. Use to highlight the binding pocket in the 3D scene and to annotate key contact residues for mechanism explanations.

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

pdb_id stringrequired — 4-character PDB identifier
ligand_code stringrequired — 3-letter chem component ID of the ligand in the structure (e.g., 'CFF')
cutoff_angstrom number — Distance cutoff in Ångströms (default 5.0, max 10.0)

Example call

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

{
  "jsonrpc": "2.0",
  "id": 1,
  "method": "tools/call",
  "params": {
    "name": "station__rcsb-org__get-binding-site",
    "arguments": {
      "pdb_id": "",
      "ligand_code": ""
    }
  }
}

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 (3062 live)
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/tools/rcsb-org__get-binding-site/raw.md — this page's Markdown twin