Protein docking can be time-consuming, especially when predictions yield a large number of unlikely conformations. One of the most common frustrations for molecular modelers is spending hours sorting through thousands of docking results only to end up discarding most due to poor interfaces or clear steric clashes.
Fortunately, there’s a way to reduce both false positives and computation time when docking in SAMSON using the Hex Extension: by setting up range angles for your receptor and ligand.
Why Range Angles Help
In Hex, docking is performed using spherical coordinates. This means the search space is vast by default—unless you constrain it. The range angles feature allows you to define cones along the intermolecular axis that limit how much the receptor and ligand can rotate during the search. By localizing the orientation space, you can focus the docking on the biologically relevant interface.
For example, if you know the likely binding site or orientation of the ligand, you can significantly limit the rotational search space. This not only speeds up the docking but can improve the accuracy of results by reducing the chance of irrelevant binding modes dominating the scoring.
How to Specify Range Angles
To define range angles, open the Hex app in SAMSON via Home > Apps > Biology > Hex. After loading your receptor and ligand, go to Advanced parameters once the Sampling method is set to Range angles.
Here, you can specify:
- Receptor angle range: Usually 45° is a good start
- Ligand angle range: Also commonly set to 45°
- Twist angle range: Optional control of ligand rotation around the central docking axis
These parameters define cones with their apexes centered on the receptor and ligand, as visualized in the interface:
The two cones illustrate the constrained search domains. Docking will be performed within this limited space, enhancing focus on the expected interaction region.
Tips for Using Range Angles Effectively
- Align your system first: Use SAMSON’s Move editors to place the ligand close to its plausible binding site.
- Don’t over-constrain: While smaller ranges reduce noise, too small an angle might prevent valid docking modes from being explored.
- Combine with filtering: Use the Bumps counter or post-processing filters to refine results even further.
Conclusion
Range angles provide a simple yet powerful way to guide docking and significantly reduce irrelevant results. The time spent defining these parameters often pays off through faster computation and more interpretable results.
To learn more about how to use range angles and other features in Hex for protein docking, check out the full tutorial here: https://documentation.samson-connect.net/tutorials/hex/protein-docking-with-hex/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.