Understanding the interactions between a ligand and its target protein remains a central challenge in molecular modeling. Once docking simulations are complete, the next step is often analysis and communication—insightfully visualizing the binding site’s key residues, detecting hydrogen bonds, and presenting the model in a way that’s both informative and easy to interpret.
If you’re using SAMSON along with the FITTED Suite extension, you already have access to a powerful combination of visualization and analysis tools. In this blog post, we guide you through the process of quickly visualizing and analyzing a protein-ligand binding site using built-in SAMSON features. These steps help you make results easier to understand and communicate—whether in meetings, publications, or collaborations.
From results to insight: visualizing interactions
After you’ve run a docking simulation (check the FITTED tutorial if you haven’t yet), SAMSON lets you:
- Color and label ligand-surrounding residues
- Display those residues in licorice or ribbon styles
- Show detected hydrogen bonds
- Identify contact surfaces and more
Step-by-step: select and visualize binding site residues
Begin by selecting the resulting ligand pose in the Document view—its name usually starts with something like 1E2K_log.mol2_DockingRun_*. With the ligand selected, go to:
Select > Biology > Binding sites → choose a suitable cutoff (e.g., 6 Å) and click OK. This will highlight all protein residues within a radius of the ligand.
You can now group these residues together using the Current Selection tool in the Document view for easy re-selection later:
Add a licorice visual model
This step enhances the clarity of ligand-surrounding residues. With the residues selected, go to:
Visualization > Visual model > Licorice
For further detail, you can color-code carbon atoms by residue number:
Select > Atoms > Carbons → Visualization > Material > Per attribute > Residue index
This adds subtle color variation to distinguish parts of the binding site.
Reveal hydrogen bonds with one click
Using the Hydrogen Bond Finder extension, you can visualize H-bonds between the ligand and receptor:
- Launch the extension, select the processed receptor and click “Set”
- Select the docked ligand and click “Add hydrogen bond visual model”
Final result: a rich visual summary
After completing these steps, you’ll have a visually precise display of:
- Receptor’s secondary structure in ribbons
- Key binding site residues in licorice form
- Color-coded atoms
- Hydrogen bond interactions
This visualization makes it easier to understand interactions and present your data clearly to colleagues, reviewers, or collaborators.
Ready to explore deeper?
Use additional tools like the Protein-Ligand Interaction Analyzer for detailed contact areas and interaction types. Together, these features remove much of the manual work involved in post-docking analysis.
📖 Learn more in the full Fitted Suite documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON here.