In molecular modeling, comparing protein structures is a frequent and essential task—whether you’re identifying conserved structural motifs, evaluating mutant effects, or building homology models. But what happens when you’re only interested in a specific structural feature, like an active site helix or a loop involved in binding?
This is where region-specific alignment becomes critical, and it’s something that SAMSON’s Protein Aligner handles with care.
Why Region-Specific Alignment Matters
Whole-protein superposition typically considers the backbone atoms of all residues, which can mask small but important differences in specific regions. For example, a pair of helices might adopt very similar conformations across two structures, while the rest of the proteins differ significantly due to flexible loops or missing domains.
In SAMSON, you can interactively select only the residues you care about and align the structures based solely on those, which gives you a more focused and meaningful comparison.
How to Align Specific Protein Regions in SAMSON
The workflow is surprisingly intuitive:
- Open the Protein Aligner from Home > Align.
- Select the protein chains or models you want to align. Make sure both are visible in your workspace.
- In the alignment panel, click and drag over the sequences to highlight the regions of interest. For example, you may want to select the first 20 residues if you’re inspecting N-terminal helices.
- Click the alignment button next to your selected region (usually displayed as a distance, e.g.,
0.0 Å). This will align the structures based on just those residues—not the whole molecule.
Tips for Better Visuals
You can use Visualization > Visual model > Ribbons to clearly see structural motifs of interest. Assign distinct ribbon models to each protein for color-coded clarity, helping you focus on aligned regions visually.
Applications
- Compare local structural elements like binding loops or helices across homologs or mutants.
- Investigate conformational changes in domains after ligand binding.
- Build more accurate constraint files for region-specific molecular dynamics simulations.
Being able to focus on what matters most—not what’s structurally irrelevant elsewhere—makes this alignment approach highly valuable for structural biology workflows.
Learn more about region-specific alignment in the Protein Aligner documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.