Modeling conformational transitions is central to understanding biomolecular function. But once paths between protein conformations are computed, how can you quickly analyze them and communicate the results? This post offers a practical look at how to visualize and interpret transition paths using the Protein Path Finder app in SAMSON, focusing specifically on understanding energy landscapes along those paths.
Once a path search is completed using ART-RRT (As-Rigid-As-Possible Rapidly-exploring Random Tree) in SAMSON, the results appear in the Results tab. Each transition path includes multiple intermediate conformations and detailed energy evaluations. But this isn’t just a data table: it’s an interactive interface for visually exploring molecular motion and energy barriers that matter in your system.
Why Energy Curves Matter
Proteins often undergo conformational changes associated with significant energy barriers. The path with the lowest energy saddle or barrier is often biologically most relevant. The Saddle value (difference between max and min energy along the path) shows how high energy intermediates get; the Barrier tells you how costly the transition is compared to the start.
These summaries help prioritize which paths are energetically feasible and may warrant deeper structural or dynamical analysis.
Hands-On: Navigating the Energy Landscape
Click on a row in the results table to activate a path. The selected path’s energy curve will be plotted automatically. You can move a slider to view structures along the path, matching each state to a specific energy on the curve.
Want to compare pathways? Use Ctrl/Cmd + Click to select multiple paths. This overlays their energy curves, making comparison straightforward. Choose the one with the lowest barrier, inspect intermediates, or study possible artifacts.
Exporting Results
Need to analyze path data externally or drop an animation into a slide deck? You’re covered. Right-click on selected paths to:
- Copy the table content or energy values to clipboard
- Export conformations along the paths into the SAMSON document
- Export the paths themselves as trajectories
Animations can be created directly from the SAMSON document by double-clicking on exported paths. You can then use the Inspector to control playback or render recordings.
Quick Tips
- Use meaningful path names or remarks for easy tracking.
- Mark paths with visually distinct colors for figure generation.
- The Export Along Paths app allows you to track specific atoms during transitions—useful for creating custom charts or overlays.
Visualizing energies and structures side by side demystifies conformational transitions and supports sharing results with collaborators more clearly. Instead of only equations and coordinates, you’ll have energy landscapes and moving molecules.
To learn more about path planning and analysis, visit the complete Protein Path Finder documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.