Skempi Tools#

Configuration File: skempi_tools.json Tool Type: Local Tools Count: 3

This page contains all tools defined in the skempi_tools.json configuration file.

Available Tools#

SKEMPI_get_mutation (Type: SKEMPITool)#

Retrieve the measured binding effect of one specific substitution in a protein-protein complex. M…

SKEMPI_get_mutation tool specification

Tool Information:

  • Name: SKEMPI_get_mutation

  • Type: SKEMPITool

  • Description: Retrieve the measured binding effect of one specific substitution in a protein-protein complex. Mutations use SKEMPI’s cleaned notation of wild-type residue, chain, position, mutant residue, e.g. ‘LI38G’ for Leu38 to Gly on chain I. Returns the wild-type and mutant Kd and the derived ddG in kcal/mol. Use SKEMPI_search_by_structure first to see which substitutions were measured. Example: pdb_id=’1CSE’, mutation=’LI38G’.

Parameters:

  • pdb_id (string) (required) PDB entry of the complex, e.g. ‘1CSE’.

  • mutation (string) (required) Substitution in SKEMPI cleaned notation, e.g. ‘LI38G’.

Example Usage:

query = {
    "name": "SKEMPI_get_mutation",
    "arguments": {
        "pdb_id": "example_value",
        "mutation": "example_value"
    }
}
result = tu.run(query)

SKEMPI_search_by_protein (Type: SKEMPITool)#

Find SKEMPI complexes and measurements involving a named protein, matched case-insensitively agai…

SKEMPI_search_by_protein tool specification

Tool Information:

  • Name: SKEMPI_search_by_protein

  • Type: SKEMPITool

  • Description: Find SKEMPI complexes and measurements involving a named protein, matched case-insensitively against both binding partners. Returns the measurements plus a summary of the ddG distribution and the list of PDB structures involved. Useful for assembling a benchmark set for one protein family. Example: name=’lysozyme’.

Parameters:

  • name (string) (required) Protein name or fragment, e.g. ‘lysozyme’, ‘barnase’, ‘trypsin’.

  • limit ([‘integer’, ‘null’]) (optional) Maximum records to return (default 50, max 500).

Example Usage:

query = {
    "name": "SKEMPI_search_by_protein",
    "arguments": {
        "name": "example_value"
    }
}
result = tu.run(query)

SKEMPI_search_by_structure (Type: SKEMPITool)#

List every experimentally measured binding-affinity mutation for a protein-protein complex in SKE…

SKEMPI_search_by_structure tool specification

Tool Information:

  • Name: SKEMPI_search_by_structure

  • Type: SKEMPITool

  • Description: List every experimentally measured binding-affinity mutation for a protein-protein complex in SKEMPI 2.0, with wild-type and mutant dissociation constants and a derived ddG in kcal/mol. Positive ddG means the mutation weakens binding. Use this to obtain measured ground truth for comparison against predicted effects from DynaMut2 or sequence-model scores. Example: pdb_id=’1CSE’. SKEMPI covers roughly 350 complexes, so many PDB entries have no measurements.

Parameters:

  • pdb_id (string) (required) PDB entry of the complex, e.g. ‘1CSE’ or ‘1VFB’.

  • only_single_mutants ([‘boolean’, ‘null’]) (optional) If true, exclude records carrying more than one substitution.

  • limit ([‘integer’, ‘null’]) (optional) Maximum records to return (default 50, max 500).

Example Usage:

query = {
    "name": "SKEMPI_search_by_structure",
    "arguments": {
        "pdb_id": "example_value"
    }
}
result = tu.run(query)