When modeling molecular interactions, demonstrating a ligand binding to a receptor is essential. But what about the reverse process? Undocking animations are just as important, especially when preparing presentations, educational content, or investigating energy release during the unbinding stage.
In SAMSON, a powerful molecular design platform, you can animate molecular undocking processes visually without writing code or running simulations. Using the built-in Undock animation, you can automatically generate realistic undocking motions with just a few clicks.
Why animating undocking matters
Many modelers focus on binding, but undocking is also crucial. It helps to:
- Visualize reverse transition pathways and induced fit reversals
- Create symmetrical animations: docking and undocking effects
- Prepare videos for teaching molecular interactions and dynamics
- Review whether docking geometry or constraints lead to realistic unbinding directions
If you’ve ever manually tried to animate a protein-ligand unbinding, you’ll know aligning structures and computing directions and amplitudes is time-consuming. SAMSON’s Undock animation simplifies this dramatically.
Creating an undock animation: how to get started
The process in SAMSON is intuitive:
- Select your objects. Select at least two nodes in your document—a receptor (typically a macromolecule) and one or more ligands or meshes to undock.
- Organize your selection. If the receptor is composed of multiple parts, move them into a folder and select that folder first.
- Apply the Undock effect. Open the Animation panel in the Animator and double-click Undock.
SAMSON will automatically compute the unbinding trajectory and amplitude. You can refine the timing by adjusting keyframes.
Customize the motion
Once the animation is added, you can fine-tune its behavior:
- Amplitude: Change how far the ligand travels by selecting the animation and using the Inspector.
- Easing curve: Control the acceleration and deceleration across keyframes by modifying the Easing curve.
- Keyframe control: Move or duplicate keyframes to highlight different phases of the unbinding.
There is no need to calculate or predict final unbound positions manually—SAMSON handles it for you.
Visual example
Here is an example of the Undock animation applied to a molecular complex:
Where to go next
You can see docking and undocking in action by exploring shareable SAMSON documents. Try looking at these examples that use the concept of docking (and could be animated in reverse with Undock):
Whether you’re creating classroom visuals or refining molecular storyboards, undocking animations help complete your narratives and explore molecular motion in more directions—not just how molecules arrive at their destinations, but how they depart.
To learn more, read the full documentation on the Undock animation in SAMSON.
SAMSON and all SAMSON Extensions are free for non-commercial use. Visit www.samson-connect.net to get SAMSON.