Understanding how a ligand exits a protein’s binding pocket is critical in molecular modeling and drug discovery. Researchers often simulate multiple unbinding pathways, but visualizing and comparing them in a clear and interpretable way can be challenging. A clean visual cue—like a trajectory line—can greatly help both in analysis and in communication.
That’s where Pathlines come in. Included as part of the Ligand Path Finder workflow in SAMSON, pathlines allow you to view the motion of the center of mass of a ligand as it moves through the protein. This helps provide both a qualitative and quantitative sense of how the molecule travels.
Why Pathlines are Useful 🧭
Suppose you’ve used the Ligand Path Finder app to generate several potential unbinding pathways from a protein-ligand complex. These paths are stored as sequences of molecular conformations. But interpreting the route of the ligand—its general direction, whether it loops back or exits in a straight line, or how it clears steric obstacles—isn’t always obvious from viewing individual states or animations.
Pathlines solve this by overlaying a continuous trace of the ligand’s center of mass, making it easier to observe spatial routes, compare trajectories between runs, and identify possible bottlenecks or transitions. Whether you’re preparing a figure for a publication or deciding which pathway to explore further with enhanced sampling or free energy calculations, pathlines offer a high-impact, low-effort visualization technique.
How to Create a Pathline
If you’ve already used the Ligand Path Finder app to generate unbinding pathways, you can follow these steps to create a pathline:
- Click on a path in the Results tab to select it.
- Right click on the path in the Document View.
- Select Path > Create Pathline.
That’s it. You’ll now see a line representing the ligand’s path, traced along the route taken by its center of mass.
Tips for Better Visualization
- You can color paths differently to distinguish among multiple pathways.
- Activate or deactivate pathlines in the Document View to see one pathway at a time for clarity.
- Combine pathlines with sampling box visualizations to assess whether the pathway sufficiently explores the exit region.
Export Options
Once you’ve created pathlines, SAMSON makes it easy to export them for use in presentations or publications. Use the built-in export tools to save static images or videos of the ligand motion along the path.
When You Should Use Pathlines
Pathlines are especially helpful when:
- You have multiple unbinding pathways and want to compare their geometry.
- The ligand’s motion is non-linear and needs to be better understood.
- You need a compact way to document or present the unbinding process.
To learn more about how pathlines integrate with the Ligand Path Finder workflow and to see other visualization options, visit the full Ligand Path Finder documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON from www.samson-connect.net.