Molecular modelers frequently face the challenge of interpreting docking results in a way that goes beyond scores and binding poses. Visualizing the ligand environment—identifying surrounding residues, interactions, and spatial organization—is a vital yet sometimes tedious part of structure-based drug design. This blog post explores how SAMSON facilitates this step through streamlined visual analysis tools provided by the FITTED Suite Extension and integrated visualization features.
Why is this important?
Once docking is complete, understanding how a ligand sits in a binding site is essential to assess binding plausibility and guide design decisions. Which residues are nearby? Are there hydrogen bonds? Does the orientation align with known SAR trends? The answers to these questions often lie in visual inspection before any complex computation is run.
If you’ve docked a ligand using the FITTED Suite in SAMSON, here’s how to quickly and effectively visualize the binding site, identify interacting residues, and color code molecular features.
Step-by-step visual exploration
Start by selecting the processed receptor in the Document view—for example, it may be named 1E2K_pro. Then, add a Ribbons representation for secondary structure visualization via the Visualization menu.
Next, select your resulting ligand (e.g., 1E2K_log.mol2_DockingRun_*) and choose Select > Biology > Binding sites. This tool will highlight surrounding residues based on spatial proximity. You can then group these selected residues under a meaningful label like “Binding site residues” for future reference.
With nearby residues selected, use the Licorice visual model to add clarity to atoms and bonds around the ligand. This makes local atomic and residue context much easier to interpret.
Enhancing clarity with colors and labels
SAMSON enables atom-level coloring by properties. For example, you can select all carbon atoms in the receptor and apply color schemes based on the residue index. This provides a clean overview of where part of a ligand is interacting relative to sequence context.
To remove visual clutter, simply uncheck structural models or visual elements in the Document view. You can also use the Inspector to fine-tune line thickness, color and shading styles of visual models as needed.
Putting it all together
These streamlined visual tools in SAMSON help you quickly move from docking results to meaningful structural insights without scripting or manual model setup. As a result, you spend more time interpreting structure-activity relationships and less time manipulating visualizations.
To dive deeper into automated protein-ligand docking with the FITTED Suite, explore the complete tutorial at https://documentation.samson-connect.net/tutorials/fitted/fitted-suite/.
SAMSON and all SAMSON Extensions are free for non-commercial use. Download the platform at https://www.samson-connect.net.