Protein docking simulations can be time-consuming, especially when exploring large conformational spaces. If you are using the Hex Extension in SAMSON for docking protein structures, there is a practical technique that can streamline your search: restricting the docking domain using range angles.
Docking search times often go up drastically when sampling is unconstrained, since Hex explores orientations of the ligand around the receptor in 3D space. By default, Hex considers the full spherical space (180-degree range angles), which is thorough but inefficient if you already have clues about the binding site.
What are range angles?
In Hex, docking is done using spherical coordinates around an axis connecting the centers of mass of the receptor and ligand. The range angle defines a spherical cone around this axis. By reducing this angle, you constrain Hex to search only in this cone, much like focusing a flashlight beam.
For example, by setting the receptor and ligand angle ranges to 45 degrees instead of 180, you reduce the search domain from a full sphere to much smaller cones, which significantly accelerates docking calculations.
When should I use range angles?
Use range angles when you have any prior knowledge of the binding interface, even if approximate:
- You know where the ligand binds on the receptor surface.
- You have a predicted or homologous binding site.
- You want to validate a specific docking hypothesis.
How to set range angles in SAMSON
Once you’ve launched the Hex Extension in SAMSON, follow these steps:
- Set your receptor and ligand (e.g., proteins 2PTC_E and 2PTC_I from the tutorial).
- Use the move tools in SAMSON (see Moving Objects) to manually place the ligand close to the expected binding site.
- Set the Sampling method to Range angles.
- Click on Advanced parameters.
- Set both Receptor angle range and Ligand angle range to 45 degrees—or less, depending on your case.
- Optionally set twist angle constraints if you want to limit rotation around the axis.
Why does this help?
Range angle constraints reduce computational overhead by narrowing down the search space to the region of biological interest. As a result, dockings run faster and are more likely to recover meaningful results with fewer irrelevant poses.
This approach is particularly useful when screening many protein-protein interactions or when docking models predicted with limited resolution. It is also an effective strategy when working on refinement or rescoring tasks based on experimental constraints.
If you’re interested in further reducing runtime, range angles can be combined with other settings like increasing Steric scan order or disabling certain post-processing steps during preliminary runs.
To learn more, visit the full tutorial here: Hex Extension – Protein Docking Tutorial.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.