skempi_affinity read
scidex.forge.skempi_affinity
Query SKEMPI 2.0 for experimental ΔΔG (change in binding free energy) measurements for mutations in protein–protein complexes. Filter by PDB accession code and/or protein/gene name. Returns mutation records with ΔΔG, ΔG_mut, ΔG_wt (kcal/mol), binding affinities, temperature, pH, and literature references. Positive ΔΔG = destabilising mutation; negative ΔΔG = stabilising. SKEMPI 2.0 covers ~7,000 entries from ~345 protein complexes — the standard reference for experimental protein–protein binding thermodynamics. Data: life.bsc.es/pid/skempi2 — public, no authentication required.
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.skempi_affinity``.",
"properties": {
"pdb_id": {
"anyOf": [
{
"maxLength": 10,
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "4-character PDB accession code to filter by (case-insensitive), e.g. '1CSE'. At least one of pdb_id or gene_symbol is required.",
"title": "Pdb Id"
},
"gene_symbol": {
"anyOf": [
{
"maxLength": 64,
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Gene symbol or protein name substring to filter by (case-insensitive). Matched against protein name and UniProt ID fields. At least one of pdb_id or gene_symbol is required.",
"title": "Gene Symbol"
},
"limit": {
"default": 50,
"description": "Maximum number of records to return (default 50, max 500).",
"maximum": 500,
"minimum": 1,
"title": "Limit",
"type": "integer"
}
},
"title": "ForgeSkempiAffinityIn",
"type": "object"
}Output schema
{
"$defs": {
"SkempiMutationRecord": {
"description": "One experimental ΔΔG record from SKEMPI 2.0.",
"properties": {
"pdb_entry": {
"description": "SKEMPI PDB entry identifier, e.g. '1CSE_E_I' (4-char PDB code + chain designators).",
"title": "Pdb Entry",
"type": "string"
},
"mutations": {
"description": "Mutation string in SKEMPI notation, e.g. 'SA1CG'. May contain comma-separated chains for multi-site mutations.",
"title": "Mutations",
"type": "string"
},
"protein_1": {
"default": "",
"description": "Name of protein 1 in the complex.",
"title": "Protein 1",
"type": "string"
},
"protein_2": {
"default": "",
"description": "Name of protein 2 in the complex.",
"title": "Protein 2",
"type": "string"
},
"uniprot_1": {
"default": "",
"description": "UniProt accession for protein 1 (semicolon-separated if multiple).",
"title": "Uniprot 1",
"type": "string"
},
"uniprot_2": {
"default": "",
"description": "UniProt accession for protein 2 (semicolon-separated if multiple).",
"title": "Uniprot 2",
"type": "string"
},
"ddg_kcal_mol": {
"anyOf": [
{
"type": "number"
},
{
"type": "null"
}
],
"default": null,
"description": "ΔΔG in kcal/mol (mutant − wild-type). Positive = destabilising; negative = stabilising.",
"title": "Ddg Kcal Mol"
},
"dg_mut_kcal_mol": {
"anyOf": [
{
"type": "number"
},
{
"type": "null"
}
],
"default": null,
"description": "ΔG of mutant complex in kcal/mol.",
"title": "Dg Mut Kcal Mol"
},
"dg_wt_kcal_mol": {
"anyOf": [
{
"type": "number"
},
{
"type": "null"
}
],
"default": null,
"description": "ΔG of wild-type complex in kcal/mol.",
"title": "Dg Wt Kcal Mol"
},
"affinity_mut_M": {
"anyOf": [
{
"type": "number"
},
{
"type": "null"
}
],
"default": null,
"description": "Affinity of mutant complex in M.",
"title": "Affinity Mut M"
},
"affinity_wt_M": {
"anyOf": [
{
"type": "number"
},
{
"type": "null"
}
],
"default": null,
"description": "Affinity of wild-type complex in M.",
"title": "Affinity Wt M"
},
"temperature_k": {
"anyOf": [
{
"type": "number"
},
{
"type": "null"
}
],
"default": null,
"description": "Experimental temperature in Kelvin.",
"title": "Temperature K"
},
"ph": {
"anyOf": [
{
"type": "number"
},
{
"type": "null"
}
],
"default": null,
"description": "Experimental pH.",
"title": "Ph"
},
"reference": {
"default": "",
"description": "PubMed ID or citation reference.",
"title": "Reference",
"type": "string"
},
"mutation_location": {
"default": "",
"description": "Mutation location annotation (e.g. 'COR', 'RIM', 'INT', 'SUR').",
"title": "Mutation Location",
"type": "string"
}
},
"required": [
"pdb_entry",
"mutations"
],
"title": "SkempiMutationRecord",
"type": "object"
}
},
"description": "Response shape for ``scidex.forge.skempi_affinity``.",
"properties": {
"query": {
"description": "Human-readable description of the applied filters.",
"title": "Query",
"type": "string"
},
"records": {
"description": "Matching ΔΔG records from SKEMPI 2.0.",
"items": {
"$ref": "#/$defs/SkempiMutationRecord"
},
"title": "Records",
"type": "array"
},
"total_found": {
"default": 0,
"description": "Total number of matching records before limit was applied.",
"title": "Total Found",
"type": "integer"
},
"not_found": {
"default": false,
"description": "True when no records matched the provided filters.",
"title": "Not Found",
"type": "boolean"
},
"source": {
"default": "SKEMPI 2.0 (life.bsc.es/pid/skempi2)",
"description": "Data source identifier.",
"title": "Source",
"type": "string"
},
"took_ms": {
"default": 0,
"description": "Wall-clock time for data fetch and filtering in milliseconds.",
"title": "Took Ms",
"type": "integer"
}
},
"required": [
"query"
],
"title": "ForgeSkempiAffinityOut",
"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/skempi_affinity' \
-H 'authorization: Bearer $SCIDEX_JWT' \
-H 'content-type: application/json' \
-d '{}'Discussion
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