One of the common challenges in molecular modeling is demonstrating how ligands or molecular fragments interact with a receptor in a clear and dynamic way. While molecular docking offers powerful insights, animating these docking events to communicate mechanisms to colleagues or include in presentations still often requires scripting or external animation tools. What if there were a simpler way?
The Dock animation in SAMSON provides a solution tailored for molecular modelers who want to visualize docking interactions directly within their modeling environment — no code needed. It lets users create smooth animations that show groups of atoms or meshes moving from their starting positions to their docked positions. The result is a clear, directional visual of molecular interactions, helpful for both understanding and explaining complex binding events.
Visualizing molecular interactions visually
The principle is simple: define a receptor and one or more docked entities (such as ligands). The Dock animation will then smoothly move the selected entities from automatically calculated start positions to their final bound conformations. It’s a tool that mimics the docking process visually — great for storytelling, teaching, or illustrating a computational workflow.
How to set it up
To begin, select the structural nodes or meshes involved in the docking:
- The first selected node will be treated as the static receptor, and the remaining nodes will move towards it.
- If your receptor is composed of multiple parts, select them all and place them in a folder. Then, use the folder as your first selected node.
Once selection is complete:
- Open the Animation panel in the Animator.
- Double-click on the Dock animation to insert it between two keyframes.
- Adjust the keyframes to control the timing and trajectory.
The movement amplitude is automatically calculated based on the spatial relation between start and end positions, but can be edited — more on that below.
Inspections and refinements
Once the animation is created, you can refine it using the Inspector panel:
- Amplitude: Adjust how far the atoms move before docking.
- Easing curve: Make the animation accelerate, decelerate, or use smooth transitions between frames.
This flexibility is especially useful when you want to emphasize particular binding kinetics or create polished visuals.
Example in action
The following image shows a typical use of the Dock animation in SAMSON, where a ligand moves into its binding pocket:
Want to see real-life applications of this animation? Check out presentations like 2AZ8 – Dock animation or 5SAT – Dock animation on SAMSON Connect.
This animation is useful not only for ligand docking but also for any scenario in which you want to represent how molecular parts converge, bind, or simply move relative to one another. And because it’s integrated directly into SAMSON, it’s part of your modeling workflow — no need to export, re-import, or lose detail.
To learn more and dive into the full documentation, visit the official page for the Dock animation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download the platform at https://www.samson-connect.net.