Protein docking can feel like searching for a small target in a very large space. When the binding site is already known—or there is a reasonable idea of where the proteins meet—letting the search explore every possible orientation may spend time evaluating poses that are unlikely to be relevant. In SAMSON, the Hex Extension lets you restrict the rotational search using range angles, while still exploring orientations around the starting arrangement.
The key is to treat this as a way to focus a search, not as a way to prove that a predicted pose is correct. A narrower search is useful only when the initial placement and biological evidence give you a sensible direction to explore.
Prepare the structures before narrowing the search
Start with a receptor and a ligand protein that are suitable for docking. The Hex tutorial’s sample contains the proteins 2PTC_E and 2PTC_I. For your own structures, clean and protonate them before docking. The preparation workflow described in SAMSON includes removing atoms with alternate locations, water, monatomic ions, and ligands when present, and adding hydrogens if they are absent. Do not replace hydrogens that already reflect a chosen protonation state.
If residues or heavy atoms are missing, the PDBFixer Extension can be used to fix a protein. Preparing the structures first matters: a constrained search cannot compensate for an input structure that is incomplete or unsuitable.
Set a useful starting orientation
Open Hex in SAMSON through Home > Apps > Biology > Hex. Set one protein as the receptor and the other as the ligand. If you expect a particular interface, first move and orient the ligand so it is near the presumed binding site. SAMSON’s Move editors can be used to translate and rotate it.
This starting arrangement is important because the range-angle limits are defined relative to the intermolecular axis connecting the origins of the two proteins. In Hex’s range-angle mode, the receptor and ligand are sampled within spherical cones around that axis. A range angle of 180 degrees means no angular constraint; a smaller value limits the orientations considered. The tutorial suggests 45 degrees as an example of a loose restriction around a starting orientation—not as a universal setting for every complex.
Choose constraints with care
In Hex, set the sampling method to Range angles, then open Advanced parameters to specify the receptor and ligand ranges. The tutorial’s example sets both to 45 degrees. You can also limit the ligand’s twist rotation about the intermolecular axis.
Use tighter limits only when you have a defensible starting orientation or interface hypothesis. If the binding site is unknown, restricting the angles too much could exclude relevant orientations. Conversely, when interface residues are known, orienting those residues toward each other and limiting the search can reduce the number of irrelevant predictions and shorten the search.
Balance speed and detail
Hex can use a low-resolution Steric scan before a higher-resolution Final search. The first phase rapidly covers the search space and retains a subset of candidate orientations; the final phase evaluates the retained candidates more finely. The documentation notes that a Steric scan order of 16–18 is sufficient in many cases and gives combinations such as 16 for the scan and 25 for the final search as practical starting points. A higher final-search order can be useful for high-resolution crystal structures with small expected conformational changes, while 25 is suggested for model-built or more flexible structures.
Post-processing can add another filter. A bumps counter reports steric clashes between non-bonded heavy-atom pairs, which you can use to filter results. Molecular-mechanics refinement is described as alpha-stage functionality in Hex; its rigid-body procedure may be unsuitable when large conformational changes are expected.
Inspect poses, not just rankings
After docking, review the clustered modes in the Results tab. Selecting a row restores that ligand conformation; you can create a conformation in the document from a result. Inspect promising poses visually and use analysis tools—such as contact-area or hydrogen-bond analysis—to assess the interface. A score or a filtered list is a starting point for interpretation, not a substitute for checking whether the pose makes structural sense.
For the complete walkthrough and parameter details, see the Protein docking with Hex tutorial.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at samson-connect.net.