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Alanine Scanning Peptides Design Guide

Alanine Scanning: Identifying Critical Binding Residues

What Is Alanine Scanning?

Alanine scanning is a systematic method used to determine which amino acids within a peptide are critical for binding or biological activity.

In this approach, each residue in a parent peptide is individually replaced with alanine (or another neutral residue). The modified peptides are then tested to evaluate changes in activity.

Why Is Alanine Scanning Important?

  • Identify key binding residues
  • Determine structure–function relationships
  • Refine minimal epitope regions
  • Support antibody and receptor interaction studies

Loss or reduction of activity after substitution indicates that the original residue plays an important role in binding.

How to Design an Alanine Scan Panel

  • Select the parent peptide sequence
  • Replace each amino acid one at a time with alanine
  • Generate a complete substitution set
  • Include wild-type peptide as control

Use Our Peptide Design Software

To automatically generate alanine substitution panels, use our Peptide Screening Tools:

https://www.biosyn.com/peptidescreeningtools.aspx

The software allows you to input a sequence and automatically create a complete alanine scan panel ready for export and synthesis.