Understanding how a ligand interacts with a receptor at the molecular level is vital in structure-based drug design. After running docking simulations, it’s often difficult to visualize results effectively, especially in complex molecular systems with multiple atoms and chains.
If you’re using the FITTED Suite extension in SAMSON to perform docking simulations (either covalent or non-covalent), you’ll be happy to know there’s a straightforward way to dive deeper into analyzing and visualizing docking results.
Make the Interaction View Clear
After performing a docking run in SAMSON using the FITTED Suite, a typical problem is that the resulting ligand pose is hard to situate relative to key residues. Fortunately, SAMSON lets you isolate and visualize the binding pocket and ligand interactions in only a few clicks. Let’s walk through how to do this.
Step 1: Add Visual Models
Select the processed receptor in the Document view (e.g., 1E2K_pro) and go to Visualization > Visual model > Ribbons. This adds a secondary structure model that shows alpha helices, beta sheets, and loops more clearly.
Now, uncheck the visibility of the receptor’s structural model so it doesn’t clutter the view. Only the ribbon model remains, making the ligand community more visible.
Step 2: Highlight Residues Around the Ligand
To highlight the residues near your ligand, select the ligand (e.g., 1E2K_log.mol2_DockingRun_*), navigate to Select > Biology > Binding sites, and choose appropriate distance settings (5–8 Å typically work well). This selects residues spatially close to the ligand.
You can then create a group from the selection using “Group” in the Document view. This is helpful if you need to reselect them later.
Step 3: Add a Licorice Model
With the binding site residues still selected, go to Visualization > Licorice to add a new visual model. This model gives clear visibility of the atomic connections in the residues.
Step 4: Color by Residue Sequence
A meaningful coloring scheme makes everything easier to interpret. Select the receptor, go to Select > Atoms > Carbons, and then use Visualization > Material > Per attribute > Residue index to assign colors based on sequence position. This helps visualize which residues are interacting with the ligand.
Why It’s Useful
This process significantly improves clarity when assessing receptor-ligand interactions. Without adding visual models and simplifying the view, molecular docking results can be overwhelming, especially for those who are new to molecular modeling. And if you’re sharing your analysis with collaborators or preparing figures, these visuals make a big difference in storytelling and clarity.
To explore more tips or details about docking with the FITTED Suite, see the full tutorial here: https://documentation.samson-connect.net/tutorials/fitted/fitted-suite/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download the SAMSON platform at https://www.samson-connect.net.