Aligning entire protein structures can be very informative—but sometimes, zooming in on a specific region tells the real story. If you’re modeling conformational variants, analyzing conserved motifs, or aligning flexible regions between homologs, whole-protein superposition might not be enough. That’s where region-specific protein alignment in SAMSON’s Protein Aligner becomes especially useful.
Here’s how to focus your alignment to just parts of the structure that matter most to you.
Why align just part of a protein?
Imagine you’re comparing hemoglobins from different species. Most of the structure aligns fairly well, but one alpha-helix of interest is slightly misaligned. You don’t need to reorient the entire protein—just focus on aligning that local region. This is essential when studying elements like:
- Highly conserved domains
- Flexible loops or binding pockets
- Mutated regions in disease-related proteins
Step-by-step: Region-specific alignment in SAMSON
Start by following the basic procedure to import proteins into SAMSON. For instance, use 1DLW and 1RTX hemoglobin structures by selecting Home > Fetch and loading the PDB IDs.
Once loaded, use Home > Align to open the Protein Aligner extension.
1. Select the alignable region
You’re interested in aligning the N-terminal alpha-helices of each structure. In the Protein Aligner window, select the first 20 residues in both sequences. Drag across the sequences or use modifier keys (Ctrl/Cmd, Shift, Alt) to fine-tune your selection:
2. Align the selection
After making your selection, click the alignment button located near the selected segment (it often displays a value like 0.0 Å). This executes an alignment that considers only the selected residues for RMSD calculation and superposition.
What happens under the hood?
Only the selected residues are used to compute the root-mean-square deviation (RMSD), and the structural alignment transformation is accordingly limited to that region. This minimizes the impact of flexible or non-conserved regions that might otherwise distort the alignment.
The visual result can be striking—previously misaligned secondary structures become clearly overlaid, improving your analysis and figures.
Tips for better clarity
- Use Visualization > Visual model > Ribbons to emphasize secondary structures.
- Apply a different visual model per protein to distinguish them by color.
- If needed, toggle on/off individual atoms in Document view for cleaner visuals.
When to use this
Region-specific alignment is especially helpful when comparing catalytic sites, aligning protein-protein interaction interfaces, or analyzing structural changes within protein families. It’s a flexible approach that complements global alignment strategies.
To explore all alignment options and examples, including sequence-based alignment or whole-protein superposition, visit the Protein Aligner documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.