Generating biologically meaningful motion pathways between molecular conformations—especially for large biomolecules—is a common challenge in structural biology and molecular modeling. When the structures differ in atom count or residue indexing, things can get especially tricky. If you’ve ever attempted to create a realistic trajectory between two experimental structures, you know how frustrating it can be to find a flexible, intuitive tool for this purpose.
In this post, we’ll explore how to generate a molecular trajectory of the SARS-CoV-2 spike protein as it transitions from a closed to an open state. This showcases the use of SAMSON, an integrative molecular design platform, to visualize such transitions smoothly—even when the involved structures differ.
Problem: Two States, Two Challenges
For the SARS-CoV-2 spike protein, structural biologists have provided two key conformational states:
These two models differ in the number of residues, making it non-trivial to interpolate conformational changes. SAMSON offers a path to handle this with custom scripting and dedicated modules like ARAP (As-Rigid-As-Possible) and P-NEB (Parallel Nudged Elastic Band).
Solution: Building a Trajectory
Here’s an overview of the workflow to generate a realistic transition from open to closed state:
- Firstly, bond orders for sugar molecules are corrected using a Python script.
- Next, the structures are prepared by adding hydrogens and performing energy minimization.
- The ARAP module is used to interpolate motion from open (6VYB) to closed (6VXX). The ARAP interpolation acts on structural geometry.
- This path is refined using the P-NEB module, which improves the results with physical consistency.
Despite differences in residue count and complexity, this method generates a dynamic, insightful visualization.
Results in Motion 🎞️
Here’s how this motion looks from three perspectives:
Side view:
Angled view:
Top view:
Export and Share
If you want to inspect the full trajectory or use it in your own work, it’s available in several formats:
If you’re curious about the technical accuracy and want to process the trajectory further, keep in mind that these animations are provided “as is.” They are excellent for visualization but should be validated for use in predictive modeling or precise energetic studies.
To learn more and view the full tutorial, visit the original documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.