Accurately comparing proteins is a cornerstone of molecular modeling, whether you’re examining point mutations, comparing homologs across species, or preparing a structure for homology modeling. But when working with multi-chain proteins or oligomeric complexes, sequence alignment at the chain level – rather than just the structural model – becomes crucial.
This blog post walks you through how to use the Protein Aligner in SAMSON to perform sequence alignment by chain. This targeted approach allows you to focus on specific chains within multi-subunit complexes. It’s particularly useful when your proteins have different domain patches, or when comparing subunits across species where chain-level differences might be functionally important.
Why Align By Chain?
Here’s a common scenario: you’ve loaded two oligomeric proteins into your modeling environment – maybe hemoglobin variants from different organisms. They both have multiple chains (say, alpha and beta subunits), and you want to examine exactly how conserved the beta subunit is. Structural alignment at the model level might obscure the differences between corresponding chains, especially if the order or number of chains differs.
This is where chain-level sequence alignment helps. By aligning chain-to-chain explicitly, you ensure you’re comparing apples to apples.
Performing the Alignment in SAMSON
To start, make sure you’ve loaded the protein structures you’re interested in. In the example below, we’re comparing chains from 1DLW and 1RTX, both hemoglobin proteins.
Once loaded, go to Home > Align to launch the Protein Aligner. You’ll see each protein’s chains listed in the interface.
Click Align sequences (by chain). SAMSON will now pair up chains with matching lengths or best matches (based on internal heuristics). This gives you a more granular alignment that respects biological subunit organization.
Visual Insights with Amino Acid Properties
To get more out of your sequence alignment, activate the residue highlighting options. Click the 
icon to toggle between conserved residue similarity, polarity and other physicochemical traits.
This view helps you not just match residues, but understand how conservation maps onto relevant biochemical features.
Interactive Residue Selection
Alignments in SAMSON aren’t only for viewing—they’re interactive. Hovering over residues reveals full names and IDs, and you can click to select shared residues across aligned chains. This is particularly helpful if you want to later export regions of high conservation or variability for experimental design.
When Should You Use Chain-Level Alignment?
- Comparing specific subunits across species (e.g., beta chains of hemoglobin in vertebrates)
- Analyzing domain swaps or engineered fusions
- Inspecting mutations within a chain without structural bias
- Preparing custom alignments for targeted drug design
Wrapping Up
Aligning by chain in SAMSON’s Protein Aligner gives you control and clarity when performing sequence comparisons. It’s a small but effective tool to reduce noise and increase biological relevance—especially in complex or multi-chain systems.
Learn more in the SAMSON documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON from https://www.samson-connect.net.