Molecular modelers studying protein-ligand interactions often get stuck after generating ligand unbinding paths: how do you analyze these trajectories, compare them, and extract valuable information such as energy barriers? If you’ve used the Ligand Path Finder in SAMSON, the good news is that the platform offers powerful ways to visualize, compare, and export energy-rich unbinding paths.
In this post, we focus on how you can make the most of your simulation results in SAMSON using the Results tab of the Ligand Path Finder tool. We’ll walk through analyzing output paths, plotting energy profiles, and exporting trajectories to share with colleagues or use in further studies. Here’s how.
Interpreting Multiple Unbinding Paths
After you’ve set up your system and run the planner, each found path is automatically added to the Results tab. The paths table presents key numerical values that let you understand the thermodynamic and conformational nature of each trajectory.
You’ll see values like:
- MinE and MaxE – minimum and maximum energies of the conformations in the path.
- Saddle – the energy barrier from the lowest to highest point (MaxE – MinE).
- Barrier – the energy barrier from the start to the highest point (MaxE – First).
- # States – the total number of conformations saved in the path.
These metrics help compare paths and decide which ones are worth further attention. For example, a path with a lower Barrier may indicate a more favorable unbinding pathway.
Viewing Energy Profiles Interactively
Clicking on any path lets you interactively explore energy changes as the ligand moves. Use the slider to move across the conformations and instantly reflect the changes in the molecular model. You can visually inspect if large energy jumps correspond to specific steric clashes or protein movements.
You can also multi-select several paths (Ctrl/Cmd + click) and plot their energy profiles together to compare multiple routes side-by-side. This is especially helpful when analyzing how different random seeds or sampling boxes influence the ligand’s exit vibrancy and energetic cost.
Exporting Results for Collaboration and Documentation
Once you’ve identified paths of interest, SAMSON offers several export options:
- Copy table content to the clipboard for quick inclusion into reports or spreadsheets.
- Copy path energy values for numerical analysis or graph building outside of SAMSON.
- Export paths as trajectories that appear in the Document view — making it easy to animate or share in presentations.
- Export conformations at regular intervals along the path to capture key structural snapshots.
These paths can be refined, visualized with pathlines (to show ligand center-of-mass), and even coupled with optimization tools like P-NEB to generate more realistic transitions.
Why This Matters
For molecular modelers, knowing that a ligand unbinds is only half the journey. Understanding how it unbinds — and with what energy cost — can help rank drug candidates, predict off-target effects, or guide mutagenesis experiments. The Ligand Path Finder’s results tools bridge the gap between raw simulation output and meaningful interpretation.
Want to go deeper or apply this to your own models? View the full documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON here.