Pepcalc Tools

Configuration File: pepcalc_tools.json Tool Type: Local Tools Count: 1

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

Available Tools

PepCalc_peptide_properties (Type: PepCalcTool)

Calculate physicochemical properties for a peptide with optional N-terminal and C-terminal chemic…

PepCalc_peptide_properties tool specification

Tool Information:

  • Name: PepCalc_peptide_properties

  • Type: PepCalcTool

  • Description: Calculate physicochemical properties for a peptide with optional N-terminal and C-terminal chemical modifications, using the Pep-Calc.com API. Returns the molecular formula, monoisotopic and average molecular weight, isoelectric point (pI), and 280 nm extinction coefficient (oxidized / reduced cysteine).

Unlike a bare-sequence calculator (e.g. ProtParam_calculate, which only accepts standard amino acids with free termini), this tool models the terminal group, so it covers synthetic / therapeutic peptides. The terminal group changes the formula, mass, and pI: for example seq=ACDEFGHIK with C_term=NH2 (amide) gives pI 6.96 and MW 1017.47, while C_term=OH (free acid) gives pI 5.23 and MW 1018.45.

N_term / C_term are chemical-group strings understood by Pep-Calc: N_term defaults to ‘H’ (free amine; ‘Ac’ for N-terminal acetyl), C_term defaults to ‘OH’ (free acid; ‘NH2’ for C-terminal amide). No API key required.

Parameters:

  • seq (string) (required) Peptide sequence in single-letter amino acid code (e.g. ‘HAEGTFTSDVSSYLEGQAAKEFIAWLVKGR’ or ‘ACDEFGHIK’).

  • N_term (string) (optional) N-terminal group as a Pep-Calc chemical string. Default ‘H’ (free amine, unmodified). Use ‘Ac’ for N-terminal acetylation.

  • C_term (string) (optional) C-terminal group as a Pep-Calc chemical string. Default ‘OH’ (free acid, unmodified). Use ‘NH2’ for C-terminal amidation.

Example Usage:

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