When Full-Protein Alignment Isn’t Enough: Focusing on Regions That Matter

In molecular modeling, aligning full protein structures is a common task—especially when comparing proteins from different organisms or assessing mutations. But what happens when you’re only interested in a specific functional domain or a particular secondary structure?

This is a frequent scenario in structure-based design and homology modeling. For example, two protein homologs may share only patchy sequence similarity, or they might have large insertions or flexible loops that skew a global alignment. Aligning the entire proteins in such cases risks overlooking important local similarities.

That’s where region-specific alignment comes in.

Why Region-Specific Alignment?

  • To compare local motifs or conserved binding pockets across homologs
  • To focus on structurally similar elements (e.g., helices or beta sheets) even when global RMSD is high
  • To better understand conformational differences in specific fragments, such as loop motions or hinge regions

How to Align Regions in SAMSON

Let’s say you’re comparing two hemoglobins—1DLW and 1RTX—and you’ve noticed that their N-terminal alpha-helices are structurally similar but misaligned in a global superposition.

Here’s how you can realign only those helices using SAMSON’s Protein Aligner extension:

  1. After loading the proteins, open Home > Align to launch the Protein Aligner.
  2. Select the first 20 residues in both sequences. You can Shift-click to select ranges or Ctrl/Cmd-click for non-consecutive residues.
  3. Click on the small alignment button (often showing 0.0 Å) next to your selection. This tells SAMSON to align only the corresponding residues.
  4. Observe how just the region of interest becomes aligned, offering a much more meaningful comparison when investigating local features.

Selecting residues for alignment

Region-specific alignment result

Tips for Better Visualization

  • Use Visualization > Visual model > Ribbons to enable ribbon display mode if it’s not already on.
  • Create a separate visual model per protein to distinguish structures by color.
  • Use the Highlight residues option to color based on similarity or polarity for easier interpretation.

Highlighting conserved residues

Real-World Applications

  • Refining homology models by iteratively aligning conserved domains
  • Mapping active or allosteric sites for drug design
  • Highlighting structural conservation in evolutionary studies

In many molecular design projects, structure alignment isn’t just about minimizing RMSD—it’s about understanding the relationship between local structure and function. SAMSON’s Protein Aligner gives you control to focus on what’s biologically meaningful, not just geometrically optimal.

To learn more about using the Protein Aligner, visit the full documentation page.

SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON here.

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