Brenda Tools

Configuration File: brenda_tools.json Tool Type: Local Tools Count: 5

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

Available Tools

BRENDA_get_enzyme_info (Type: BRENDATool)

Get general enzyme information from BRENDA by EC number. Returns enzyme name, systematic name, an…

BRENDA_get_enzyme_info tool specification

Tool Information:

  • Name: BRENDA_get_enzyme_info

  • Type: BRENDATool

  • Description: Get general enzyme information from BRENDA by EC number. Returns enzyme name, systematic name, and catalyzed reaction. Requires free BRENDA account (register at brenda-enzymes.org/register.php).

Parameters:

  • operation (string) (optional) Operation type (fixed: get_enzyme_info)

  • ec_number (string) (optional) EC number (e.g., 1.1.1.1)

  • enzyme_id (string) (optional) Alias for ec_number. Enzyme identifier in EC notation (e.g., 1.1.1.1).

Example Usage:

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

BRENDA_get_enzyme_kinetics (Type: BRENDATool)

Get comprehensive enzyme kinetic parameters WITHOUT requiring BRENDA credentials. Retrieves enzym…

BRENDA_get_enzyme_kinetics tool specification

Tool Information:

  • Name: BRENDA_get_enzyme_kinetics

  • Type: BRENDATool

  • Description: Get comprehensive enzyme kinetic parameters WITHOUT requiring BRENDA credentials. Retrieves enzyme identity (name, catalytic activity, alternative names) from ExPASy ENZYME and kinetic parameters (Km, kcat, Ki, Vmax, kcat/Km) from SABIO-RK. If BRENDA credentials are set (BRENDA_EMAIL, BRENDA_PASSWORD), additionally fetches optimal pH, optimal temperature, and specific activity from BRENDA. Accepts EC number (e.g., 1.1.1.1) or enzyme name (e.g., alcohol dehydrogenase). Returns aggregated summary statistics across all reported values plus individual measurements with substrate specificity and organism information.

Parameters:

  • operation (string) (optional) Operation type (fixed: get_enzyme_kinetics)

  • ec_number (string) (optional) EC number (e.g., 1.1.1.1 for alcohol dehydrogenase, 2.7.1.1 for hexokinase, 3.4.21.5 for thrombin)

  • enzyme_name (string) (optional) Enzyme common name. Will be resolved to EC number via UniProt. Examples: alcohol dehydrogenase, hexokinase, lactate dehydrogenase, thrombin

  • organism (string) (optional) Optional organism filter (e.g., Homo sapiens, Escherichia coli, Saccharomyces cerevisiae)

  • enzyme_id (string) (optional) Alias for ec_number. Enzyme identifier in EC notation.

  • limit ([‘integer’, ‘null’]) (optional) Maximum number of SABIO-RK kinetic law entries to retrieve (default 20)

Example Usage:

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

BRENDA_get_inhibitors (Type: BRENDATool)

Get enzyme inhibitor data from BRENDA. Returns inhibitor names and Ki (inhibition constant) value…

BRENDA_get_inhibitors tool specification

Tool Information:

  • Name: BRENDA_get_inhibitors

  • Type: BRENDATool

  • Description: Get enzyme inhibitor data from BRENDA. Returns inhibitor names and Ki (inhibition constant) values in mM with organism information. Lower Ki means more potent inhibition. Requires free BRENDA account (register at brenda-enzymes.org/register.php).

Parameters:

  • operation (string) (optional) Operation type (fixed: get_inhibitors)

  • ec_number (string) (optional) EC number

  • organism (string) (optional) Optional organism filter

  • enzyme_id (string) (optional) Alias for ec_number. Enzyme identifier in EC notation (e.g., 1.1.1.1).

Example Usage:

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

BRENDA_get_kcat (Type: BRENDATool)

Get kcat (turnover number) values from BRENDA enzyme database. kcat is the maximum number of subs…

BRENDA_get_kcat tool specification

Tool Information:

  • Name: BRENDA_get_kcat

  • Type: BRENDATool

  • Description: Get kcat (turnover number) values from BRENDA enzyme database. kcat is the maximum number of substrate molecules converted to product per enzyme per second. Returns values in 1/s. Requires free BRENDA account.

Parameters:

  • operation (string) (optional) Operation type (fixed: get_kcat)

  • ec_number (string) (optional) EC number

  • organism (string) (optional) Optional organism filter

  • enzyme_id (string) (optional) Alias for ec_number. Enzyme identifier in EC notation (e.g., 1.1.1.1).

Example Usage:

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

BRENDA_get_km (Type: BRENDATool)

Get Km (Michaelis constant) values from BRENDA enzyme database. Km indicates substrate affinity -…

BRENDA_get_km tool specification

Tool Information:

  • Name: BRENDA_get_km

  • Type: BRENDATool

  • Description: Get Km (Michaelis constant) values from BRENDA enzyme database. Km indicates substrate affinity - lower Km means higher affinity. Returns values in mM with organism and substrate information. Requires free BRENDA account (register at brenda-enzymes.org/register.php).

Parameters:

  • operation (string) (optional) Operation type (fixed: get_km)

  • ec_number (string) (optional) EC number (e.g., 1.1.1.1 for alcohol dehydrogenase, 2.7.1.1 for hexokinase)

  • organism (string) (optional) Optional organism filter (e.g., ‘Homo sapiens’, ‘Escherichia coli’)

  • enzyme_id (string) (optional) Alias for ec_number. Enzyme identifier in EC notation (e.g., 1.1.1.1).

Example Usage:

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