Protein docking simulations can be time-consuming, especially when you’re working with large biomolecular systems or exploring vast conformational spaces. A common struggle among molecular modelers? Waiting for docking runs that search everywhere when the relevant binding site is already known. Fortunately, SAMSON’s Hex Extension provides a clear way to focus your docking: range angles.
When performing docking simulations in the Hex Extension, the default is often to explore the entire orientation space—effectively rotating the ligand around the receptor across all possible positions. This is helpful when you have no prior knowledge, but in many typical scenarios (e.g., known binding pockets, homology models), it’s wasteful.
What Are Range Angles?
Range angles allow you to define spherical cones around a default docking axis (between the receptor and ligand) in which the docking algorithm will search. This means you’re telling Hex: “Look only around this orientation, because that’s what matters.” The default is 180°, which covers everything—but smaller values like 45° sharply reduce the search space.
In SAMSON, you can set these values inside the Hex app by clicking Advanced parameters, as shown below:
Why This Matters
Besides faster docking times, range angles reduce the number of false positives and focus the predictions around likely interaction areas. This is particularly helpful when you manually pre-orient a ligand near its predicted or known binding site.
How to Use Range Angles Effectively
- Before setting them, pre-position your ligand near the expected binding site using SAMSON’s transformation tools (e.g., translate and rotate editors).
- In the Hex app, go to Advanced parameters.
- Change the receptor and ligand range angles to something like 45°.
- Adjust the twist angle if applicable—this constrains the rotation about the docking axis.
- Launch the docking simulation.
When set correctly, you will see visual cones representing the angular search domains:
Practical Tip
This strategy works best when you have structural clues about the interface—e.g., from experimental data, homologous complexes, or surface matching algorithms. Using range angles won’t just speed up your simulation; it will likely improve the quality of your results when applied correctly.
If you’re using Hex within SAMSON and skipping this step, you’re probably wasting computation time—especially when docking known protein partners or working with curated ligands and receptors. Try using range angles next time and see how much smoother your workflow becomes.
To learn more, visit the full documentation page for the Hex Extension: https://documentation.samson-connect.net/tutorials/hex/protein-docking-with-hex/
SAMSON and all SAMSON Extensions are free for non-commercial use. Download SAMSON at https://www.samson-connect.net