Understanding how proteins change shape between two conformations is a challenge faced by many molecular modelers. These conformational changes are essential for protein function, but identifying plausible transition pathways and analyzing their energy profiles can be time-consuming and complex.
The Protein Path Finder app in SAMSON simplifies this task. It leverages the ART-RRT algorithm, a method combining T-RRT sampling with ARAP-based motion modeling and constrained minimization. But once you’ve found a transition path, one practical question remains: how do you make sense of the results?
In this blog post, we’ll focus on a common modeling bottleneck: how to interpret, visualize, and export the results of conformational path searches using the Protein Path Finder app.
What’s included in the results?
After running the planner, the Results tab displays a summary table, which includes key metrics for each path found:
- MinE: minimum energy along the path (kcal/mol)
- MaxE: maximum energy
- Saddle: MaxE − MinE
- Barrier: MaxE − First (initial state energy)
- Time: how long the search took
These fields help evaluate whether a path is energetically reasonable, and whether it’s worth refining via other methods, such as parallel NEB.
Plotting energy profiles
Select any path in the results table to reveal its energy curve. You can move the slider to inspect each conformation and its corresponding UFF energy in the viewport.
Want to compare multiple paths at once? Use Ctrl/Cmd + click to select several rows, and you’ll be able to see overlapping energy curves — making it easier to identify the lowest-barrier transition.
Exporting the data
The app provides flexible export options under the Results tab:
- Copy the table content (or just selected rows) to your clipboard via right-click.
- Export energy values along a path using Copy path energy.
- Convert paths to trajectories inside the same SAMSON document using the Export paths button.
- Export the full set of conformations along a path with customizable intervals using the Export button.
If your goal is to use the transition path in another tool or create animations, these export features make handing off your data a lot easier — no need to manually extract coordinates.
Final tips
- Double-click a path to play/pause its animation in the viewport.
- Use the Inspector to fine-tune playback and appearance.
- Check out the dedicated Pathlines tutorial to track center-of-mass movements.
With these tools, you can go beyond just finding a pathway—you can fully explore, evaluate, and communicate your results.
Learn more in the full documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.