Protein–protein docking can produce a long list of plausible-looking poses, especially when the search explores many possible orientations. If you already have a reasonable idea of where the proteins interact, searching every direction may spend time on orientations that are unlikely to be useful. A practical way to focus the calculation is to start the ligand near the suspected binding site and restrict its angular search.
This does not prove that a pose is correct. It is a way to use existing structural knowledge to define a more focused search, while remembering that an overly narrow search can exclude the answer you are looking for.
Start with structures you can interpret
Before opening Hex in SAMSON, prepare the receptor and ligand structures. Remove atoms with alternate locations, water, monatomic ions, and other ligands if present. Add hydrogens if they are missing, but do not replace hydrogens that were already added according to a chosen protonation state. If residues or heavy atoms are missing, the PDBFixer Extension can help repair the protein; it can also add hydrogens for a specified pH.
These steps matter because docking results depend on the structures supplied to the calculation. For your own proteins, clean and protonate them before docking. The tutorial sample uses the structural models 2PTC_E and 2PTC_I; its waters have already been removed and hydrogens added.
Use what you know to define the search
In the Hex app, assign one protein as the receptor and the other as the ligand. If you may want to repeat the calculation with different settings, save the ligand’s starting conformation first. Then set the Sampling method to Range angles and open Advanced parameters.
Hex describes the search using spherical coordinates. The range-angle settings limit the receptor and ligand orientations around the intermolecular axis connecting their origins. A range angle of 180 degrees leaves the full sphere available; a smaller value restricts the orientations sampled to a cone around the starting direction. In the tutorial, both ranges are set to 45 degrees as an example of a limited search.
If the binding site is known, first move and orient the ligand near that site. SAMSON’s Move editors can be used to translate and rotate it. Then choose range angles that keep the search focused around this starting arrangement. The twist angle can also limit rotation about the intermolecular axis.
The image shows the geometric idea: the cones are centered on the protein origins, with the intermolecular axis connecting them. The settings are most useful when your initial orientation is informative. If the ligand is pointed away from the suspected site, a narrow cone may simply prevent Hex from sampling relevant orientations. When the binding site or starting pose is uncertain, broader ranges are a safer choice.
Balance focus and coverage
Range angles are only one part of the search. Hex also offers correlation choices, such as shape-only or shape plus electrostatics. Electrostatics may be useful when the proteins have complementary formal charges, but the documentation advises against using it for docking DNA or RNA. The search can also include a low-resolution Steric scan followed by a finer Final search. The tutorial notes that a steric-scan order of 16–18 is often sufficient and gives 16 for the scan and 25 for the final search as a combination that works well in many cases. These are starting points, not universal settings; consult the interface tooltips and Hex manual for other parameters.
After running the calculation, inspect the clustered results rather than treating the top score as a definitive answer. The Results tab lets you view the best mode per cluster or all modes. Selecting a row restores its ligand conformation; you can also create a conformation in the document. Compare promising poses with visual models, measurements, and interaction analysis. For example, SAMSON’s Protein-Ligand Interaction Analyzer can compute contact area and hydrogen bonds, while the Hydrogen Bond Finder can display hydrogen bonds between the receptor and ligand.
The useful habit is to make the search reflect what you know, then check whether the resulting poses remain structurally plausible. A focused search can save effort, but its conclusions are only as reliable as the starting structures, assumptions, and follow-up analysis.
Read the full Hex protein-docking tutorial for the complete workflow and parameter details.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.