One of the common frustrations in protein-protein docking is the large number of false positives that arise from unconstrained searches. Molecular modelers often spend excessive time manually filtering docking results, only to realize that many of the proposed orientations are physically unreasonable or biologically irrelevant. Fortunately, there’s an effective solution built directly into the Hex Extension for SAMSON: range angles.
Range angles allow you to focus the docking search by providing spatial constraints on how ligand and receptor interact. Instead of exploring all possible orientations over a sphere, you can restrict the search to specific cones defined by user-specified rotation limits. This significantly cuts down on computation time and improves the relevance of results.
What Are Range Angles?
The Hex docking algorithm performs searches in spherical coordinates. By default, it considers full 180° rotations for both ligand and receptor—essentially the entire sphere. This is appropriate when you have no prior knowledge about interaction interfaces, but it often leads to a noisy result set.
By constraining the angular search space, you define a spherical cone along the intermolecular axis connecting the centers of both proteins. Only those orientations within the cone will be explored.
When to Use Range Angles
- You have an idea of the binding site location. Perhaps from prior experiments, literature, or homology modeling.
- You already pre-oriented your ligand close to the receptor’s binding interface.
- You want to reduce runtime and enhance docking accuracy.
How to Enable and Use Range Angles in Hex
After loading your system in SAMSON and launching the Hex app via Home > Apps > Biology > Hex, follow these steps:
- Set the sampling method to Range angles.
- Click on Advanced parameters.
- Assign a range angle for both the receptor and ligand. A value like 45° is a good starting point.
- (Optional) Adjust the twist rotation range around the intermolecular axis.
By specifying, for instance, a 45° cone for each protein, you’re telling Hex to only look within that tighter region of orientations. Visually, you’ll see cones drawn in the 3D workspace illustrating the search domains.
If you already positioned the ligand near the presumed binding site, this restriction will further hone in on plausible interactions and discard implausible ones.
Benefits You Might Notice
- Faster docking: Smaller search space means reduced computational complexity.
- Cleaned-up results: Fewer false-positive orientations to manually inspect.
- More focused energy landscape: Helps clustering pick up meaningful local minima.
Practical Tip
Use SAMSON’s Move editors to manually pre-orient molecules before defining your angle cones. Orient the ligand toward the suspected binding interface on the receptor, then apply your range constraints accordingly.
👉 Want to further explore optional parameters like twist rotation and sampling resolution? You’ll find those in the Advanced parameters panel of Hex for even finer control.
To learn more about this and other features in the Hex Extension, visit the full documentation page:
https://documentation.samson-connect.net/tutorials/hex/protein-docking-with-hex/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.