A protein-docking run can produce many candidate poses, and a broad search may spend time exploring orientations that are unlikely to matter. If you already have evidence about where two proteins bind, you can use that knowledge to narrow the search. The benefit is a more focused calculation; the trade-off is that an overly restrictive search can exclude plausible poses.
This workflow uses Hex in SAMSON to set angular limits around an initial receptor–ligand arrangement. It is most useful when you have a reasonable idea of the binding region and can orient the ligand toward it before docking. If the binding site is unknown, or your starting arrangement is unreliable, restrictive limits may be counterproductive.
Prepare the structures before searching
Start with a receptor and a ligand. Before docking, remove atoms with alternate locations, and remove water, monatomic ions, and ligands if they are present and not needed for the calculation. Add hydrogens if they are missing. If hydrogens already reflect a chosen protonation state, do not change them casually. Structures with missing residues or heavy atoms may need repair; the SAMSON documentation points to the PDBFixer extension for this task.
In SAMSON, open the Hex app from Home > Apps > Biology > Hex. Select the receptor in the document and click Set as receptor; then select the ligand and set it as ligand. Save the ligand’s initial conformation before running a search if you may want to repeat the calculation with different parameters.
Use prior knowledge to focus the search
In Hex, choose Range angles as the sampling method and open Advanced parameters. Docking is performed using spherical coordinates around the intermolecular axis connecting the origins of the two proteins. A range angle of 180 degrees leaves the full sphere available. A smaller angle restricts orientations to a cone around that axis.
If you know the likely interface, first move and orient the ligand near the binding site using a SAMSON Move editor. Then try a receptor range angle of 45 degrees and a ligand range angle of 45 degrees. These are example settings from the tutorial, not universal defaults: the right limits depend on how confidently you know the interface and how accurately the starting pose is oriented.
You can also constrain the ligand’s twist rotation about the intermolecular axis. Treat each restriction as an assumption about the pose, not merely as a speed setting: if the assumed direction is wrong, the search may miss relevant solutions.
Choose resolution with the structure in mind
Hex can perform a coarse Steric scan followed by a finer Final search. The first phase rapidly evaluates orientations at lower resolution and retains promising candidates for the next phase. The tutorial reports that a Steric scan order of 16–18 is sufficient in many cases, and gives combinations such as N=16 for the scan with N=25 for the final search, or N=20 followed by N=30.
For the Final search, N=25 is generally suggested for model-built or more flexible structures, while N=30 is recommended for high-resolution crystal structures when binding-related conformational changes are expected to be small. Higher-resolution searches can take longer. These settings are starting points; consult Hex’s tooltips and manual for the full parameter descriptions.
Read results as candidates, not answers
After the calculation, inspect the Results tab. Modes are clustered, and you can view the best-scoring mode in each cluster or all modes. Selecting a row restores that ligand conformation; right-clicking a row and choosing Create conformation adds it to the document.
A score or cluster is a way to organize docking candidates, not experimental confirmation. Examine promising poses visually and, where useful, check steric clashes, distances, contacts, and hydrogen bonds. Hex offers a bumps counter for steric clashes. Its molecular-mechanics refinement is described as alpha-stage and is best avoided when large conformational changes are expected, because it can eject ligands with incorrect conformations from the binding site.
For a step-by-step walkthrough and further parameter details, see the Protein docking with Hex tutorial.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.