One of the most frequent pain points in protein-protein docking is the overwhelming number of false positives that can result from broad, unconstrained docking searches. If you already have some structural knowledge about your proteins—like the approximate location of binding sites—then a full angular search might be overkill, both in terms of time and accuracy.
Thankfully, SAMSON and the Hex Extension allow you to focus your docking experiments using a feature called range angles, which limits the sampling space during docking. This simple tweak can dramatically reduce computational costs and improve the likelihood of success.
What Is a Range Angle?
Range angles define a spherical cone centered along the axis that connects the centers of the receptor and ligand. By default, this is set at 180°, which means no angular constraint—the ligand can search the entire surface of the receptor. But this can lead to excessive false positives and long docking times.
Instead, setting the range to something like 45° focuses the search on a specific interface region. This is especially useful if binding regions are known or hypothesized from experimental data or previous studies.
How to Set Up Range Angles in SAMSON
- In the Hex app, set the Sampling method to Range angles.
- Click on Advanced parameters.
- Set both Receptor angle range and Ligand angle range to 45° (or another value of your choice).
You’ll see two cones appear on the screen, each centered on the respective protein. These cones visually describe the constrained angular space being used for the simulation.
Tip: Use Prior Knowledge About the Binding Site
If you already know approximately where the interaction takes place, take a moment to manually reorient your ligand toward the binding site using the Move editors. After that, choose a narrow angle for both receptor and ligand—this way, you’re not only reducing false positives but also speeding up the docking process.
Why Control the Search Domain?
- Efficiency: Smaller search spaces equal shorter computation times.
- Precision: Narrowing the search reduces irrelevant docking poses.
- Better results: Focuses sampling on the region of biological interest.
Docking, particularly in rigid-body approaches like Hex, hinges on efficient and targeted sampling. Managing the angular search domain is one of the simplest yet most effective ways to get better docking results faster.
To learn more, check out the full tutorial documentation page: 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.