Protein-ligand docking is only half the story. Once a docking run completes successfully, understanding how your ligand interacts with the receptor is critical — not only to validate the result, but also to extract meaningful insights. That’s where visual analysis comes in.
The SAMSON molecular design platform offers a comprehensive set of tools that allow molecular modelers to quickly gain structural insight into ligand-receptor interactions. This post walks through a useful workflow: visualizing and interpreting the results of a protein-ligand docking run performed with the FITTED Suite in SAMSON. The goal is to help you transition from results to understanding — efficiently.
Common Friction: Understanding the Binding Site Clearly
After a docking run, molecular modelers often need to:
- Reveal how a ligand fits into its binding site
- Understand nearby residues and possible interactions
- Communicate findings visually with annotated snapshots
Without standardized tools and clear procedures, this often requires tedious manual steps or switching between different software. Using visual models in SAMSON remedies that.
Step-by-Step: Exploring the Binding Site
1. Add a Secondary Structure Visual Model
After docking, the receptor (e.g. 1E2K_pro, the processed form of your protein) can be selected in the Document view. With this selected, apply the Ribbons visual model:
You can now hide the atomic view and retain a clean, structural perspective of the protein fold.
2. Highlight the Binding Site Residues
Next, select the ligand result, then go to Select > Biology > Binding sites to automatically select nearby residues. These are stored in a group (e.g. “Binding site residues”), which helps manage selection later.
3. Apply Licorice Representation
The selected residues around the ligand can then be displayed via Licorice style for clearer visualization of interactions:
You can also colorize atoms, such as carbons, by residue index to reflect continuity across the protein.
4. Optional: Hydrogen Bonds
Using the Hydrogen Bond Finder extension, you can visualize H-bonds between ligand and protein for both validation and publication purposes:
Final Thoughts
This streamlined visualization process not only saves time but also enhances your ability to interpret and communicate key docking results. Instead of manually inspecting distances or fumbling between representations, SAMSON provides tailored visual cues to make sense of the 3D complexity of molecular interactions.
To explore further tools, analysis extensions, and customization options, you can browse the full documentation for the FITTED Suite in SAMSON.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.