When exploring ligand unbinding pathways from protein structures, an often-overlooked—but critical—detail is how you define the sampling box. This box guides the algorithm by specifying where it should explore potential exit routes for the ligand. If it’s misaligned or incorrectly sized, even the most sophisticated search methods can miss relevant paths.
In SAMSON’s Ligand Path Finder, the sampling box defines the spatial region in which the method searches for pathways by manipulating a subset of atoms called ARAP active atoms. If you’re not careful, setting this region too narrowly (or in a direction opposite of where the ligand could feasibly exit the protein) can lead to inefficient or unrealistic sampling.
Why It Matters
Picture the sampling box as the ‘playground’ for the ligand’s movement. This region must be large enough to encompass realistic exit routes, but not so big that it wastes computational resources exploring irrelevant areas. In cases like membrane proteins, for example, an incorrect box orientation could entirely miss the permeation pathway toward the extracellular space or cytosol.
In the sample system provided by the Ligand Path Finder tutorial—Lactose permease bound to Thiodigalactosid (TDG)—the system is already aligned along the Z-axis. This default orientation simplifies the task: you can set the sampling box along the Z direction to favor unbinding toward the periplasmic space (expected in this protein). SAMSON helps get you started by automatically suggesting box dimensions that encompass both the ligand and protein atoms, but you always have control to alter these dimensions.
How to Set It
After preparing the system and defining the ARAP atoms, navigate to the Set the sampling region box:
A green box appears in the Viewport, representing the defined sampling region:
You can interactively change the box dimensions to fit your system’s orientation and biological relevance. For example, if unbinding is likely to occur through a pore or external channel, orient the box along that tunnel and extend the box accordingly.
Tips for Better Sampling Setup
- Always align your system with Cartesian axes before setting the sampling box. Use SAMSON’s Move editors for this.
- If unsure about the exit pathway, test multiple orientations and run the planner a few times for each.
- Use minimal yet sufficient extension—avoid over-expanding the box unless you expect distant exit points.
Why This Saves Time
Cleverly defining your sampling box can dramatically reduce the number of failed samples and increase the biological relevance of your results. It narrows down the search space while boosting the success rate of uncovering meaningful paths. It’s a small setup step that pays off in accuracy and efficiency.
To explore ligand migration in proteins more effectively, visit the Ligand Path Finder tutorial.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON here.