Understanding how molecular structures change their conformation during biological processes is a key challenge in molecular modeling. This is especially relevant for large and complex structures like the SARS-CoV-2 spike protein. One of the most frequent user pains among molecular modelers is the difficulty of visualizing such conformational changes without spending hours building trajectories or configuring animations manually.
If you’re working with viral structures or protein mechanisms and you wish you could see what a transition from a closed to an open form actually looks like, this animation-based approach using SAMSON might make your work faster and more visual.
The SARS-CoV-2 virus infects cells through a spike protein that binds to the ACE2 receptor on human cells. This spike protein moves from a closed (inactive) state to an open (active) state to initiate infection. Accurately simulating and visualizing that opening motion is crucial to understanding the infection mechanism, and potentially designing therapeutic interventions.
In SAMSON, this motion has been computed from experimentally resolved structures—6VXX (closed state) and 6VYB (open state)—and interpolated into a continuous transition trajectory. The result: intuitive 3D animations that show what happens when the spike activates.
Animating the Opening Motion
As shown below, the spike transitions from a tightly closed form to an open conformation where one of the three spike proteins is lifted, exposing the receptor-binding domain needed for infection. These animations are not just informative—they can be directly inspiring for presentations, research visualizations, or hypothesis testing.
Side view of the transition:
Oblique angle view:
Top view:
These dynamic views allow you to appreciate the asymmetric lifting of one unit of the trimeric spike complex—something that’s difficult to grasp from static structures alone.
Download and Adapt the Trajectory
The trajectory files are openly available and can be explored or modified for your use case:
By using the SAMSON file, you can also manipulate the animation interactively—double click to play or pause, explore individual conformations, and integrate them into further modeling workflows.
These animations are a useful aid for presentations and for anyone studying how viral proteins undergo conformational changes. They can also serve as a foundation for deeper calculations like docking, dynamics simulations, or epitope mapping.
Learn more and access all media and data at the official documentation page.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.