Forge Tools brenda_enzyme

brenda_enzyme read

scidex.forge.brenda_enzyme

Query BRENDA (Braunschweig Enzyme Database) for experimentally measured enzyme kinetics and substrate data by EC number or enzyme name. Returns Km (substrate affinity), kcat (turnover number), Vmax (maximum velocity), substrate lists, inhibitors, and activators from peer-reviewed literature. Essential for metabolic modelling and experiment feasibility assessment. Complements KEGG pathways (topology) with actual measured kinetic constants. Input: EC number (e.g. '1.1.1.1') or enzyme name; optional organism filter; data_types list (km_values, kcat_values, vmax_values, substrates, inhibitors, activators); limit for kinetic entries. Auth: set BRENDA_EMAIL and BRENDA_PASSWORD env vars (free academic registration at brenda-enzymes.org). API: BRENDA SOAP (https://www.brenda-enzymes.org/soap/brenda_server.php).

HTTP: POST /api/scidex/forge/brenda_enzyme

Invoke

Calls scidex.tool.invoke on the substrate with this tool name. Edit the JSON below — it must match the input schema. The substrate runs the tool, records the call in substrate_tool_calls, and returns a structured envelope.

Sign in to invoke this tool. Schema and curl snippet are visible to anyone.

Schemas

Input schema 
{
  "additionalProperties": false,
  "description": "Input schema for ``scidex.forge.brenda_enzyme``.",
  "properties": {
    "query": {
      "description": "EC number (e.g. ``'1.1.1.1'``) or enzyme name (e.g. ``'alcohol dehydrogenase'``). EC numbers are preferred for precise BRENDA lookup.",
      "maxLength": 100,
      "title": "Query",
      "type": "string"
    },
    "organism": {
      "anyOf": [
        {
          "maxLength": 200,
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Optional organism filter (e.g. ``'Homo sapiens'``, ``'Escherichia coli'``). Applied client-side: only entries whose organism field contains this string (case-insensitive) are returned. Pass ``None`` (default) to return all organisms.",
      "title": "Organism"
    },
    "data_types": {
      "description": "Data types to retrieve from BRENDA. Valid values: ``'km_values'``, ``'kcat_values'``, ``'vmax_values'``, ``'substrates'``, ``'inhibitors'``, ``'activators'``. Default: ``['km_values', 'substrates']``.",
      "items": {
        "type": "string"
      },
      "title": "Data Types",
      "type": "array"
    },
    "limit": {
      "default": 20,
      "description": "Maximum number of kinetic entries (``results``) to return. Does not cap ``substrates`` or ``inhibitors`` lists. Default 20.",
      "maximum": 200,
      "minimum": 1,
      "title": "Limit",
      "type": "integer"
    }
  },
  "required": [
    "query"
  ],
  "title": "ForgeBRENDAEnzymeIn",
  "type": "object"
}
Output schema 
{
  "$defs": {
    "BRENDAKineticEntry": {
      "description": "One experimentally measured kinetic parameter entry from BRENDA.",
      "properties": {
        "parameter": {
          "description": "Kinetic parameter type: ``'km_value'``, ``'kcat_value'``, or ``'vmax_value'``.",
          "title": "Parameter",
          "type": "string"
        },
        "value": {
          "description": "Measured value of the kinetic parameter.",
          "title": "Value",
          "type": "number"
        },
        "unit": {
          "default": "",
          "description": "Unit of the kinetic parameter (e.g. ``'mM'``, ``'1/s'``, ``'µmol/min/mg'``). May be empty when not reported by BRENDA.",
          "title": "Unit",
          "type": "string"
        },
        "substrate": {
          "default": "",
          "description": "Substrate for which the kinetic constant was measured.",
          "title": "Substrate",
          "type": "string"
        },
        "organism": {
          "default": "",
          "description": "Organism in which the measurement was performed.",
          "title": "Organism",
          "type": "string"
        },
        "commentary": {
          "default": "",
          "description": "Experimental context or additional commentary from BRENDA.",
          "title": "Commentary",
          "type": "string"
        }
      },
      "required": [
        "parameter",
        "value"
      ],
      "title": "BRENDAKineticEntry",
      "type": "object"
    }
  },
  "description": "Response shape for ``scidex.forge.brenda_enzyme``.",
  "properties": {
    "ec_number": {
      "default": "",
      "description": "EC number of the queried enzyme (e.g. ``'1.1.1.1'``). Empty string when the query did not resolve to an EC number.",
      "title": "Ec Number",
      "type": "string"
    },
    "enzyme_name": {
      "default": "",
      "description": "Recommended name of the enzyme, when available from BRENDA.",
      "title": "Enzyme Name",
      "type": "string"
    },
    "results": {
      "description": "Kinetic parameter entries (Km, kcat, Vmax) from BRENDA, capped at ``limit``.",
      "items": {
        "$ref": "#/$defs/BRENDAKineticEntry"
      },
      "title": "Results",
      "type": "array"
    },
    "substrates": {
      "description": "Distinct substrates the enzyme can process.",
      "items": {
        "type": "string"
      },
      "title": "Substrates",
      "type": "array"
    },
    "inhibitors": {
      "description": "Known inhibitors for this enzyme.",
      "items": {
        "type": "string"
      },
      "title": "Inhibitors",
      "type": "array"
    },
    "not_found": {
      "default": false,
      "description": "True when BRENDA returned no data for the queried EC number or enzyme name.",
      "title": "Not Found",
      "type": "boolean"
    },
    "source": {
      "default": "BRENDA (brenda-enzymes.org)",
      "description": "Data source attribution.",
      "title": "Source",
      "type": "string"
    }
  },
  "title": "ForgeBRENDAEnzymeOut",
  "type": "object"
}

curl snippet

Replace $SCIDEX_JWT with a valid bearer token. Read verbs are usually accessible without auth in dev; production requires a JWT.

curl -sS -X POST '/api/scidex/forge/brenda_enzyme' \
  -H 'authorization: Bearer $SCIDEX_JWT' \
  -H 'content-type: application/json' \
  -d '{
  "query": ""
}'

Discussion

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