protparam

name	protparam
description	Calculate protein parameters (MW, pI, extinction coefficient) and generate purification recommendations. Use when the user asks about protein properties, molecular weight, isoelectric point, extinction coefficients, or purification strategies.
allowed-tools	Bash(protparam_cli:*) Bash(protparam:*)

Protein Parameters Calculator

Calculate protein biophysical parameters and generate purification recommendations.

CLI Usage

Use the CLI at scripts/protparam_cli.py:

Basic Usage

scripts/protparam_cli.py --sequence MKTAYIAKQRQISFVKSH...

With Purification Recommendations

scripts/protparam_cli.py --sequence MKTAYIAKQRQISFVKSH... --purification

JSON Output

scripts/protparam_cli.py --sequence MKTAYIAKQRQISFVKSH... --json

Options

• --sequence, -s: Amino acid sequence in single letter code (required)
• --purification, -p: Include purification recommendations
• --json: Output results as JSON

Parameters Calculated

1. Basic Properties

   • Sequence length (amino acids)
   • Molecular weight (Da)
   • Theoretical isoelectric point (pI)

2. Spectroscopic Properties

   • Molar extinction coefficient at 280nm (M-1cm-1)
   • Absorbance 0.1% (1 g/L)

3. Tag Detection

   • His6 tag
   • MBP (Maltose Binding Protein)
   • GST (Glutathione S-Transferase)
   • SUMO tag

4. Cleavage Site Detection

   • TEV protease (ENLYFQ/S)
   • 3C/PreScission protease (LEVLFQ/GP)
   • Thrombin (LVPR/GS)
   • SUMO protease (Ulp1)

Purification Recommendations

When --purification is enabled, provides recommendations for:

• Affinity chromatography column (HisTrap, Amylose, GSTrap)
• Tag cleavage strategy
• Ion exchange column (Q or S based on pI)
• Concentrator MWCO
• Size exclusion column (S75, S200, Superose 6)