If you’re trying to understand how a ligand might leave a protein’s binding pocket, the Ligand Path Finder app in SAMSON offers a powerful method to simulate ligand unbinding pathways. But there’s one subtle yet crucial step that can make or break your results: defining the sampling box.
The sampling box determines the region of space in which the ART-RRT method allows the ligand to explore possible unbinding directions. Think of it as setting the stage where the drama of ligand dissociation plays out.
Why This Matters
The ART-RRT planner doesn’t explore conformational space blindly—it samples new states in a defined spatial region for the ligand. If your box is too small, the ligand may never fully leave the binding site. If it’s too large, you could waste computational time exploring irrelevant areas.
Worse, a poorly positioned box could bias the sampling away from the most feasible exit path. That’s why setting this box thoughtfully—based on your protein’s geometry and orientation—is essential.
How to Do It in SAMSON
Once you’ve loaded your system and defined the ligand, active and fixed atoms using the Ligand Path Finder app, navigate to the Set the sampling region section of the app interface.
The app will suggest default dimensions that enclose the ligand and the surrounding protein atoms. These can be a good starting point—but they’re just that: a starting point.
You can manually adjust the box dimensions to focus sampling in a specific direction. For instance, in the provided tutorial example, the system is already oriented with the Z-axis pointing toward the periplasmic side of the protein. Setting the sampling box to bias motion along this axis helps explore likely unbinding pathways effectively.
This green box (shown below) visually confirms the sampling region, so you can assess whether it’s well-positioned relative to the ligand pocket.
Tips for Effective Sampling Box Design
- Use visual cues: Rotate or translate your model so that a likely unbinding path aligns well with one axis (e.g., Z). This makes defining a box much easier.
- Test different box dimensions: Trying slightly different orientations or sizes can reveal alternate pathways.
- Compare paths: Run multiple searches with varied boxes and compare the resulting energy landscapes to identify consistent escape routes.
Conclusion
Defining the sampling box isn’t just a setup formality; it shapes what the algorithm can find. Careful selection can help you discover unbinding paths that are relevant, energetically reasonable, and physically meaningful. For more details on applying this method in your models, visit the full documentation of the Ligand Path Finder app here.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.