Mcsa Tools#

Configuration File: mcsa_tools.json Tool Type: Local Tools Count: 2

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

Available Tools#

MCSA_get_entry (Type: MCSATool)#

Retrieve an enzyme’s catalytic machinery from M-CSA, the curated Mechanism and Catalytic Site Atl…

MCSA_get_entry tool specification

Tool Information:

  • Name: MCSA_get_entry

  • Type: MCSATool

  • Description: Retrieve an enzyme’s catalytic machinery from M-CSA, the curated Mechanism and Catalytic Site Atlas. Returns the catalytic residues with their PDB and UniProt numbering and the role each plays in the mechanism (nucleophile, proton donor, electrostatic stabiliser and so on), plus the EC number and reaction. ToolUniverse covers enzyme function through BRENDA, Rhea and UniProt, but nothing else identifies which specific residues do the catalysis. Example: mcsa_id=2 (class A beta-lactamase).

Parameters:

  • mcsa_id ([‘integer’, ‘string’]) (required) M-CSA entry identifier, e.g. 2. Runs from 1 to roughly 1000.

Example Usage:

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

MCSA_search_enzymes (Type: MCSATool)#

Search M-CSA for enzymes by name, EC number prefix, or reference UniProt accession. Example: ec_n…

MCSA_search_enzymes tool specification

Tool Information:

  • Name: MCSA_search_enzymes

  • Type: MCSATool

  • Description: Search M-CSA for enzymes by name, EC number prefix, or reference UniProt accession. Example: ec_number=’3.5.2’ finds beta-lactamases; enzyme_name=’lysozyme’ finds the lysozyme families. The M-CSA API ignores server-side filters, so entries are scanned page by page under an explicit budget: metadata reports entries_scanned, catalogue_size and scan_complete, so a partial scan is never mistaken for an exhaustive one. Raise max_pages to 11 to cover the whole catalogue.

Parameters:

  • enzyme_name ([‘string’, ‘null’]) (optional) Substring of the enzyme name, e.g. ‘lysozyme’.

  • ec_number ([‘string’, ‘null’]) (optional) EC number or prefix, e.g. ‘3.5.2’ or ‘3.5.2.6’.

  • uniprot_id ([‘string’, ‘null’]) (optional) Reference UniProt accession, e.g. ‘P62593’.

  • max_pages ([‘integer’, ‘null’]) (optional) Catalogue pages to scan, 100 entries each (default 4, max 11 which is the full catalogue).

  • limit ([‘integer’, ‘null’]) (optional) Maximum matches to return (default 25).

Example Usage:

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