After completing a protein docking calculation, molecular modelers often ask themselves: how reliable is this result? Which ligand pose should I consider most promising? How is the ligand interacting with the protein? If you’ve used the Hex Extension in SAMSON, you may already have a list of docking poses. But the key to valuable insight lies in what you do next—analyzing and interpreting the results effectively.
SAMSON offers several built-in tools and Extensions to help you navigate this step. In this post, we’ll walk through practical strategies you can use to explore protein-ligand docking results and filter meaningful conformations using visualization and interaction analysis tools.
Visualizing the Results
After your docking finishes, the Results tab in the Hex app shows a table of possible ligand conformations. You can view all modes or just the best ones (lowest energy per cluster). Selecting a row updates the conformation in the viewport.
Want to keep a specific conformation? Just right-click on the corresponding row and choose Create conformation. You can now use it in subsequent analysis steps or include it in visualizations.
If you like animations, you can even launch one using the animation tools at the bottom of the Results tab. This mode cycles through docked poses dynamically.
Probing Interactions
One of the more powerful Extensions for analysis is the Protein-Ligand Interaction Analyzer. It lets you compute:
- Contact areas
- Hydrogen bonds (H-bonds)
- Ligand-surrounding residues
- Other interaction parameters
There’s also the Hydrogen Bond Finder, a highly focused tool for identifying intra- or inter-molecular H-bonds. Select the receptor, specify the relevant settings, and then choose the ligand to visualize the resulting hydrogen bonds—useful for ligand optimization or validation.
These tools aren’t just for checking off a box. They provide a deeper look at why a particular docking pose is energetically favorable and can help you choose between multiple results with similar scores.
Improving Engagement with Your Results
Adding visual models—like ribbons, Gaussian surfaces, or hydrophobicity maps—can help you better see where and how the ligand fits. For instance, if you’re matching a conformation with low bumps and high interaction area, rendering hydrophobic regions might clarify whether the binding region matches expectations biologically.
You can also measure distances between specific atoms or residues, identify salt bridges, or even compute the buried surface area—without leaving SAMSON.
Conclusion
Interpreting docking results isn’t about looking at a single score. With tools inside SAMSON like the Protein-Ligand Interaction Analyzer and the Hydrogen Bond Finder, you can explore the atomic story behind your docking results. Pair these tools with thoughtful visualizations to go from data to decision.
Learn more in the full tutorial.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.