Forge Tools thermomutdb_stability

thermomutdb_stability read

scidex.forge.thermomutdb_stability

Query ThermoMutDB for experimentally measured protein thermal stability changes (ΔΔG in kcal/mol, ΔTm in °C) caused by point mutations. Accepts a UniProt accession (e.g. 'P00533' for EGFR, 'P04637' for TP53) or a 4-character PDB entry ID (e.g. '1IVO'). Each record includes the mutation (e.g. 'A96V'), ΔΔG, ΔTm, pH, temperature, experimental method (DSC/CD/fluorescence), and PubMed ID. Covers 14,000+ mutations across 1,600+ proteins from peer-reviewed literature. Essential for protein engineering, variant effect prediction, and stability-guided drug design. Complements alphafold_structure (3-D coordinates) with the measured thermodynamic effect of each mutation. API: https://biosig.lab.uq.edu.au/thermomutdb/ — free, no authentication required.

HTTP: POST /api/scidex/forge/thermomutdb_stability

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.thermomutdb_stability``.",
  "properties": {
    "uniprot_or_pdb": {
      "description": "UniProt accession (e.g. ``'P00533'`` for EGFR, ``'P04637'`` for TP53) or 4-character PDB entry ID (e.g. ``'1IVO'``). Case-insensitive.",
      "maxLength": 20,
      "title": "Uniprot Or Pdb",
      "type": "string"
    },
    "limit": {
      "default": 50,
      "description": "Maximum number of mutation records to return.",
      "maximum": 500,
      "minimum": 1,
      "title": "Limit",
      "type": "integer"
    }
  },
  "required": [
    "uniprot_or_pdb"
  ],
  "title": "ForgeThermoMutDBStabilityIn",
  "type": "object"
}
Output schema 
{
  "$defs": {
    "ThermoMutRecord": {
      "description": "One experimentally measured stability change record from ThermoMutDB.",
      "properties": {
        "mutation": {
          "description": "Point mutation in single-letter amino acid notation (e.g. 'A96V' = Ala96→Val).",
          "title": "Mutation",
          "type": "string"
        },
        "ddG": {
          "anyOf": [
            {
              "type": "number"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Change in unfolding free energy (ΔΔG) in kcal/mol. Negative values indicate destabilisation; positive values indicate stabilisation.",
          "title": "Ddg"
        },
        "dTm": {
          "anyOf": [
            {
              "type": "number"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Change in melting temperature (ΔTm) in °C. Negative values indicate destabilisation.",
          "title": "Dtm"
        },
        "uniprot_id": {
          "default": "",
          "description": "UniProt accession for this measurement.",
          "title": "Uniprot Id",
          "type": "string"
        },
        "pdb_id": {
          "default": "",
          "description": "PDB entry ID for this measurement.",
          "title": "Pdb Id",
          "type": "string"
        },
        "chain": {
          "default": "",
          "description": "PDB chain identifier for the mutation.",
          "title": "Chain",
          "type": "string"
        },
        "pH": {
          "anyOf": [
            {
              "type": "number"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Experimental pH at which the measurement was taken.",
          "title": "Ph"
        },
        "temperature": {
          "anyOf": [
            {
              "type": "number"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Experimental temperature (°C) at which the measurement was taken.",
          "title": "Temperature"
        },
        "method": {
          "default": "",
          "description": "Experimental method used (e.g. 'DSC', 'fluorescence', 'CD').",
          "title": "Method",
          "type": "string"
        },
        "pubmed_id": {
          "default": "",
          "description": "PubMed ID of the supporting publication.",
          "title": "Pubmed Id",
          "type": "string"
        }
      },
      "required": [
        "mutation"
      ],
      "title": "ThermoMutRecord",
      "type": "object"
    }
  },
  "description": "Response shape for ``scidex.forge.thermomutdb_stability``.",
  "properties": {
    "query": {
      "description": "The UniProt accession or PDB ID that was queried.",
      "title": "Query",
      "type": "string"
    },
    "mutations": {
      "description": "Experimentally measured stability change records (limited to ``limit``).",
      "items": {
        "$ref": "#/$defs/ThermoMutRecord"
      },
      "title": "Mutations",
      "type": "array"
    },
    "total_found": {
      "default": 0,
      "description": "Total number of mutation records found before the limit was applied.",
      "title": "Total Found",
      "type": "integer"
    },
    "not_found": {
      "default": false,
      "description": "True when ThermoMutDB has no records for the queried UniProt ID or PDB ID.",
      "title": "Not Found",
      "type": "boolean"
    },
    "source": {
      "default": "ThermoMutDB (biosig.lab.uq.edu.au/thermomutdb)",
      "description": "Data source attribution.",
      "title": "Source",
      "type": "string"
    }
  },
  "required": [
    "query"
  ],
  "title": "ForgeThermoMutDBStabilityOut",
  "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/thermomutdb_stability' \
  -H 'authorization: Bearer $SCIDEX_JWT' \
  -H 'content-type: application/json' \
  -d '{
  "uniprot_or_pdb": ""
}'

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