Choosing the right sampling region is a crucial step when exploring ligand unbinding pathways in molecular modeling. This step directly influences the direction in which the ligand is permitted to move and the quality of the unbinding paths found. In SAMSON’s Ligand Path Finder app, this is achieved using a sampling box to define the region through which active ARAP atoms are allowed to move.
But what exactly makes a sampling box “effective”? And how do you avoid the common pitfall of restricting plausible unbinding directions without realizing it?
Why the Sampling Box Matters
The sampling box defines the spatial domain where the planner searches for ligand unbinding paths. If it’s too tight, potential exits may be missed. Too broad, and computation time could rise significantly without necessarily improving insights.
Since the direction of exploration is biased by the shape and orientation of the sampling box, its placement should reflect your expectations—or hypotheses—about likely exit channels. Ideally, the box should also align with structural features of the protein, such as channels or known binding pockets.
How to Set It Up in SAMSON
To define the sampling box in SAMSON, simply expand the Set the sampling region section once you’ve selected the active ARAP atom(s). By default, SAMSON suggests a box large enough to enclose the ligand and protein atoms, but you can adjust the values manually to guide the search more specifically.
In the example provided in the tutorial, the sampling box is intentionally extended along the Z-axis to favor unbinding toward the periplasmic side of the protein. This is a strong design choice based on biological insight.
Tips for Practical Use
- 🧭 Align your system first: Make sure the system is properly oriented along the Cartesian axes before defining the box. Use SAMSON’s Move editors or coordinate alignment tools to do this.
- 🔬 Visualize the channel: Use structural insights or literature data to prioritize expected exit pathways. This can help you size and position the sampling box accordingly.
- 🎯 Focus the search: You can define asymmetric box dimensions (e.g., longer in one direction) to bias unbinding in a specific direction if certain paths are improbable due to sterics or energetics.
- 🎥 Observe the effect: After setting the box, visualize it (it’s rendered as a green box) and make sure it covers plausible egress routes for the ligand. If you frequently obtain failed or trapped paths, reassess the box dimensions and placement.
When (and Why) to Modify the Defaults
Default values are useful as starting points but might not suit particular systems, especially if the protein has a known tunnel or if the ligand is deeply buried. Periodically reassessing whether the sampling box aligns with biological intuition or simulation goals not only improves the relevance of results but can also reveal alternative binding/unbinding pathways.
Carefully setting the sampling box increases the chances of visualizing plausible ligand egress routes while reducing time wasted on unproductive sampling. Especially when combined with appropriate active and fixed ARAP atom selections, the sampling box is one of your strongest tools for extracting useful insight from unbinding mechanisms.
To learn more about the full Ligand Path Finder workflow, including how to define ligand atoms, ARAP groups, and run the planner, visit the Ligand Path Finder documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.