When studying protein conformational changes, it’s not enough to know the start and end states. Understanding how a protein moves between these states—through what pathways and at what energetic cost—is key for applications like drug design, enzyme engineering, or understanding allosteric transitions. But analyzing, visualizing, and exporting this transition data can be tricky. If you’ve ever thought, “I found the paths, now what?”—this post is for you.
In this guide, we’ll show you how the Protein Path Finder app in SAMSON helps you meaningfully explore and visualize protein transition pathways once they’ve been computed. SAMSON makes it easier to view energy profiles along a path, navigate conformations, and export the data for presentations or further analysis.
Why Post-Processing Matters 🧪
After computing conformational transition pathways using the ART-RRT method, researchers often need to:
- Compare multiple pathways in terms of energy profiles
- Identify energy barriers or saddle points
- Visualize intermediate conformations along a path
- Share results with collaborators or include them in publications
All of the above is supported by the Results tab in the Protein Path Finder app.
Inspecting and Interpreting Paths
As paths are found, they appear in a table showing key information: the number of states in each path, minimum and maximum energies, saddle energies (MaxE – MinE), barriers (MaxE – First), and more.
To explore the energy curves:
- Click a row in the table to load its data.
- Use the slider below to scroll through the conformations along the selected path.
- The corresponding conformation will appear in the main viewport, with energy shown in the Universal Force Field window.
- Multi-select paths with Ctrl/Cmd + Click to compare paths side by side.
Exporting Energy Data and Structures
There are several export options:
- Copy table content: Select one or more paths, right-click, choose “Copy table content” to export the entire set of numeric details into your clipboard.
- Copy path energy: Right-click to export just the energy values along each conformation of the path.
- Export paths: Generate full molecular trajectories of transitions and add them to the SAMSON document for visualization or further refinement (e.g., via P-NEB).
- Export conformations: Export selected conformations along a path with adjustable intervals (e.g., every 5th state).
You can also double-click on any path label in the Document view to start or stop an animation. For more control, select the path and open the Inspector. Right-clicking a path brings up a contextual menu with additional export and visualization options.
Why It’s Handy
These options allow you to:
- Compare energy efficiency of different transitions
- Create visually intuitive animations and plots
- Share conformational changes with collaborators who may not use SAMSON
These capabilities are especially useful if you’re preparing figures, assessing mechanistic plausibility, or trying to rank different pathways by energetic feasibility.
Learn more in the full documentation: SAMSON Protein Path Finder Tutorial.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON from https://www.samson-connect.net.