Comparing entire protein structures can be useful – but sometimes, you only care about a specific segment. Whether you’re studying conserved motifs, flexible binding domains, or comparing specific helices across two species, aligning full structures may dilute the insights you’re looking for.
That’s where region-specific protein alignment comes in. In SAMSON, the Protein Aligner extension lets you superimpose proteins not just globally – but locally – by aligning only selected residues. This short guide introduces you to this feature and how it can help you focus your structural analysis where it matters most.
Why align part of a protein instead of the whole thing?
Imagine you’re working with homologous proteins from two organisms that share a common fold, but differ substantially in their surface regions. Or maybe you’re interested in comparing the shape and position of a specific alpha-helix involved in ligand binding. Whole-protein alignment might reduce the accuracy of your comparison by introducing irrelevant structural noise.
Region-specific alignment helps you:
- Compare conserved secondary structure elements more precisely.
- Focus on segments relevant to function (e.g., binding domains, motifs).
- Reduce RMSD bias introduced by poorly conserved flexible regions.
How to perform region-specific alignment in SAMSON
Let’s say you’ve loaded two protein structures (e.g., 1DLW and 1RTX) into SAMSON and launched the Protein Aligner extension via Home > Align.
Once inside the Protein Aligner interface, the alignment view provides direct access to both sequence and structure visualization. For region-specific alignment:
- Select the residues you want to align – either directly from the sequence or interactively from the 3D model in the viewport.
- You can select the same range in both proteins (e.g., the first 20 residues).
- Click the alignment button that appears next to your selected residues. The two structures will now be superimposed based on those specific regions only.
Here’s a visual example from the SAMSON documentation, where two alpha-helices are aligned based on a 20-residue selection:
Tips for working with selected regions
- Use Shift to select consecutive residues or Ctrl/Cmd for non-consecutive ones.
- Highlight chemical or physical properties of aligned residues via the highlight icon to better interpret similarity.
- Combine ribbon visualizations with coloring schemes to differentiate aligned regions clearly.
When is local alignment most useful?
This feature is particularly relevant when:
- Studying subdomains of multi-domain proteins.
- Comparing active sites of enzymes across homologs.
- Analyzing evolutionary conservation of functionally critical regions.
It’s a precise approach for structural bioinformatics, homology modeling, or comparative protein analysis workflows.
For step-by-step guidance, more screenshots, and advanced options, visit the full documentation: Protein Aligner Documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.