Streamline Protein Sequence Alignment with SAMSON’s Protein Aligner.

Protein sequence alignment is a critical step for molecular modelers solving a variety of structural and functional questions. However, aligning sequences and comparing structures often involve juggling between different tools and formats, which can be time-consuming and error-prone. SAMSON’s Protein Aligner aims to simplify this process by integrating these capabilities into a single workflow, allowing you to align sequences, inspect conserved residues, and superimpose structures seamlessly.

Why Sequence Alignment Matters

The precise alignment of protein sequences is essential for several applications, including:

  • Pinpointing conserved residues critical for biological function or ligand binding.
  • Analyzing structural differences between species or mutants.
  • Building reliable homology models for subsequent molecular design workflows.

SAMSON’s Protein Aligner delivers all these functionalities within minutes, streamlining your projects and ensuring reproducibility.

Step-by-Step Guide to Protein Sequence Alignment in SAMSON

Here’s how you can align protein sequences step by step using SAMSON’s built-in tools:

1. Loading Your Proteins

To begin, fetch or open the proteins to be compared. For example, if you’re working with two hemoglobins from different organisms (1DLW and 1RTX):

  • Go to Home > Fetch in SAMSON.
  • Enter 1DLW 1RTX under PDB or PDB (mmCIF) and click Load.

Fetch PDBs

Pro tip: If your structures contain extra solvent, ligands, or alternate locations, consider cleaning them using the Protein Preparation & Validation extension.

2. Launching Protein Aligner

Once the proteins are ready:

  • Click Home > Align to launch the Protein Aligner. You’ll see an intuitive interface displaying your loaded proteins.

Protein Aligner Interface

3. Performing Sequence Alignment

The Protein Aligner offers two primary modes for sequence alignment:

  • Align sequences (by structure): Aligns one entire structural model to another.
  • Align sequences (by chain): Aligns individual chains within models. This is especially helpful for structures containing multiple chains, such as protein oligomers.

Choose your alignment mode and click the respective Align sequences button to generate the alignment:

Align sequences

4. Interpreting Results

Once aligned, you can highlight amino acid properties (e.g., polarity or conservation) for further inspection. Toggle these visualization options under the Highlight residues settings:

Highlight residues

Hovering over a residue will display its name and ID. Clicking on it selects that residue and links it to its aligned partners across sequences. This enables quick exploration of functionally important regions.

5. Exporting and Next Steps

Once your sequence alignment is complete, consider leveraging the results for downstream workflows:

  • Export the alignment to support homology modeling tasks.
  • Map conserved residues onto ligand-binding sites or use them to design inhibitors or activators.
  • Use the same workflow for comparative analysis of additional proteins or additional chains.

Learn More

The Protein Aligner not only simplifies sequence alignment but also bridges the gap between sequence and structure analysis. It’s part of the integrated SAMSON platform, designed to make molecular modeling workflows efficient and intuitive. For a comprehensive guide to the Protein Aligner, visit the official tutorial at this link.

Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get your free version at SAMSON Connect.

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