Forge Tools mcsa_catalytic

mcsa_catalytic read

scidex.forge.mcsa_catalytic

Look up curated catalytic residues and reaction mechanisms from M-CSA (Mechanism and Catalytic Site Atlas, EBI/Thornton group). Accepts an EC number (e.g. '3.4.21.64') or PDB ID (e.g. '1CSE'). Returns M-CSA entry records with per-residue function annotations (nucleophile, acid/base, electrophilic activator, etc.) and mechanism literature references. Covers >1,000 enzyme families with experimentally validated annotations. Complements forge_brenda_enzyme (kinetics) and forge_cath_domains (structure). API: https://www.ebi.ac.uk/thornton-srv/m-csa/api/ — public, no auth required.

HTTP: POST /api/scidex/forge/mcsa_catalytic

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.mcsa_catalytic``.",
  "properties": {
    "query": {
      "description": "EC number (e.g. ``3.4.21.64``) or PDB ID (e.g. ``1CSE``). The query type is auto-detected: EC numbers match ``d+.d+.d+.[d-]+``; all other 4-character tokens are treated as PDB IDs.  Shorter/longer strings trigger an EC-number search.",
      "maxLength": 20,
      "minLength": 1,
      "title": "Query",
      "type": "string"
    },
    "limit": {
      "default": 10,
      "description": "Maximum number of M-CSA entries to return (1–50). Default 10.",
      "maximum": 50,
      "minimum": 1,
      "title": "Limit",
      "type": "integer"
    }
  },
  "required": [
    "query"
  ],
  "title": "ForgeMCSACatalyticIn",
  "type": "object"
}
Output schema 
{
  "$defs": {
    "MCSACatalyticResidue": {
      "description": "One catalytic residue annotation from M-CSA.",
      "properties": {
        "residue_name": {
          "description": "Three-letter residue code (e.g. 'CYS', 'HIS').",
          "title": "Residue Name",
          "type": "string"
        },
        "residue_number": {
          "default": "",
          "description": "Sequence number in the PDB chain.",
          "title": "Residue Number",
          "type": "string"
        },
        "chain": {
          "default": "",
          "description": "PDB chain identifier.",
          "title": "Chain",
          "type": "string"
        },
        "functions": {
          "description": "Assigned catalytic function labels, e.g. 'nucleophile', 'acid/base', 'electrophilic activator', 'leaving group'.",
          "items": {
            "type": "string"
          },
          "title": "Functions",
          "type": "array"
        }
      },
      "required": [
        "residue_name"
      ],
      "title": "MCSACatalyticResidue",
      "type": "object"
    },
    "MCSAEntry": {
      "description": "One M-CSA entry — an enzyme with its catalytic site annotation.",
      "properties": {
        "mcsa_id": {
          "description": "M-CSA entry identifier (e.g. '1').",
          "title": "Mcsa Id",
          "type": "string"
        },
        "pdb_id": {
          "default": "",
          "description": "Representative PDB accession (e.g. '1CSE').",
          "title": "Pdb Id",
          "type": "string"
        },
        "ec_number": {
          "default": "",
          "description": "EC number (e.g. '3.4.21.64').",
          "title": "Ec Number",
          "type": "string"
        },
        "enzyme_name": {
          "default": "",
          "description": "Enzyme / protein name from M-CSA.",
          "title": "Enzyme Name",
          "type": "string"
        },
        "catalytic_residues": {
          "description": "Curated catalytic residue records with function labels.",
          "items": {
            "$ref": "#/$defs/MCSACatalyticResidue"
          },
          "title": "Catalytic Residues",
          "type": "array"
        },
        "mechanism_reference": {
          "default": "",
          "description": "Literature DOI or reference describing the catalytic mechanism.",
          "title": "Mechanism Reference",
          "type": "string"
        },
        "mcsa_url": {
          "default": "",
          "description": "Direct URL to the M-CSA entry.",
          "title": "Mcsa Url",
          "type": "string"
        }
      },
      "required": [
        "mcsa_id"
      ],
      "title": "MCSAEntry",
      "type": "object"
    }
  },
  "description": "Response shape for ``scidex.forge.mcsa_catalytic``.",
  "properties": {
    "query": {
      "description": "The query string that was submitted.",
      "title": "Query",
      "type": "string"
    },
    "entries": {
      "description": "M-CSA entries matching the query.",
      "items": {
        "$ref": "#/$defs/MCSAEntry"
      },
      "title": "Entries",
      "type": "array"
    },
    "not_found": {
      "default": false,
      "description": "True when the M-CSA API returned no entries for the query.",
      "title": "Not Found",
      "type": "boolean"
    },
    "source": {
      "default": "M-CSA (ebi.ac.uk/thornton-srv/m-csa)",
      "description": "Data source attribution string.",
      "title": "Source",
      "type": "string"
    },
    "took_ms": {
      "default": 0,
      "description": "Wall-clock time for the upstream API call.",
      "title": "Took Ms",
      "type": "integer"
    }
  },
  "required": [
    "query"
  ],
  "title": "ForgeMCSACatalyticOut",
  "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/mcsa_catalytic' \
  -H 'authorization: Bearer $SCIDEX_JWT' \
  -H 'content-type: application/json' \
  -d '{
  "query": ""
}'

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