Analyzing protein-ligand interactions is a crucial step in molecular modeling and drug design. After performing docking simulations, it is equally important to visually interpret the results for better insights into the molecular interactions. SAMSON, with its advanced visualization tools, makes this process straightforward. This blog post will guide you on how to leverage SAMSON’s features to effectively visualize and analyze your docking outcomes.
Adding a Secondary Structure Visual Model
To begin, the first step in making the receptor visually comprehensible is to add a ribbons representation for its secondary structure. Here’s how you can do it:
- In the Document view, select the processed receptor, for instance,
1E2K_pro. - Click on Visualization > Visual model > Ribbons to add a secondary structure visual model.
- You can then hide the original structural model by unchecking it in the Document view.
With the ribbons representation, the overall protein structure becomes much clearer, allowing you to focus on the relevant regions like the binding site.
Highlighting the Binding Site
Another way to enhance visualization is by adding visual representations for residues surrounding the ligand. Here are the steps:
- Select the ligand, for example,
1E2K_log.mol2_DockingRun_*. - Go to Select > Biology > Binding sites and define the radius of selection (e.g., 5 Å).
- Create a group for the selected residues by right-clicking on the current selection in the Document view and choosing Create group.
- With the binding site residues selected, go to Visualization > Visual model > Licorice to add a detailed representation of those residues.
You can further enhance this by customizing colors for carbons in the receptor based on residue sequences or other attributes. The result provides a clear depiction of the receptor-ligand interaction area.
Analyzing Interactions with Hydrogen Bonds
Visualizing hydrogen bonds is a powerful way to explore ligand-receptor interactions. Using the Hydrogen Bond Finder extension in SAMSON, you can display H-bonds between the ligand and receptor. Here’s the process:
- Select both the receptor (e.g.,
1E2K_pro) and the ligand (e.g.,1E2K_log.mol2_DockingRun_*). - In the Hydrogen Bond Finder, choose the “… in the current selection and the system” option.
- Add a new hydrogen bond visual model by clicking Add hydrogen bond visual model.
Once added, you can inspect and adjust parameters of the H-bond model, such as distance, through the Inspector. This step significantly enhances your understanding of molecular interactions.
Conclusion
By combining SAMSON’s various visualization tools—such as ribbons for secondary structures, licorice visuals for binding sites, and hydrogen bond models—you can gain deeper insights into protein-ligand docking results. Whether you are working on non-covalent or covalent docking studies, these features help simplify complex molecular interactions and foster informed decision-making in drug design.
To explore these features in depth, visit the original documentation: FITTED Suite in SAMSON.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get started today by downloading SAMSON from here.