When running protein-ligand docking simulations, getting results is only the first step. The real challenge often lies in interpreting those results—especially for complex systems—and sharing them in a clear and insightful way.
If you've tried to analyze docking poses in raw molecular structures, you probably know how quickly things can get messy: overlapping atoms, hard-to-trace residues, unclear binding interactions. But if you use SAMSON and the FITTED Suite, there's an integrated, visual solution worth exploring.
Why Visualization Matters After Docking
Visual analysis can reveal things that tables of RMSD values or score rankings can't. By viewing the ligand in context—seeing its fit in the binding pocket, identifying residues within interaction distance, coloring structural motifs—we can answer core questions about binding mode, specificity, and even unexplored optimization opportunities.
Step-by-Step: Visualizing a Docked Protein-Ligand Complex
Once you've completed a docking run with the FITTED Suite (e.g., self-docking of TMC 500 in the 1E2K system), here’s a typical visual workflow inside SAMSON:
1. Add Secondary Structure (Ribbon View)
Select the processed receptor (e.g., 1E2K_pro), and use the Visualization > Visual model > Ribbons menu. This replaces the default atomistic mess with clean helices, sheets, and loops. To keep things neat, you can hide the raw structural model by unchecking it in the Document view.
2. Highlight the Binding Site in Detail
Select the docked ligand (e.g., 1E2K_log.mol2_DockingRun_*) and run Select > Biology > Binding sites to automatically pick up neighboring residues. From there, you can save those atoms as a group—easy to revisit later—and add a Licorice visual for clarity.
3. Color by Property (Optional, but Useful)
Want to color atoms (e.g., just carbons) by residue index or chain? That’s helpful for distinguishing domains or tracking proximity. Select the atoms, then choose Visualization > Material > Per attribute > Residue index. Now different regions of your protein take on distinct hues.
4. Annotate Hydrogen Bonds
To explore H-bond interactions, use the Hydrogen Bond Finder extension. Apply it to your ligand and receptor, and filter via distance or angle as needed. The resulting visual adds dotted lines with donor/acceptor labels that update live with your 3D model.
5. Inspect Contacts and Scores
For a slightly more quantitative layer, the Protein-ligand Interaction Analyzer shows contact areas, interacting residues, and a quick summary of all scored positions. It’s a solid complement to the visuals.
Tips for Better Interpretation
- Use groups and labels for clarity and to organize complex scenes.
- Switch off unnecessary visuals (e.g., water, hydrogens) while doing structural comparisons.
- Export views or record videos to explain your conclusions to others—teams, supervisors, or the community.
By adopting these practices, molecular modelers can go from docking results to discussions grounded in clear evidence. Better visuals mean better science, better collaboration, and often, better hypotheses.
You can find more details and examples on the official documentation page: https://documentation.samson-connect.net/tutorials/fitted/fitted-suite/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.