Protein–protein docking can feel like searching for one useful arrangement in a vast space of possible orientations. When the binding site is already known—or you have a reasonable starting pose—searching every direction may spend time exploring orientations that are unlikely to be relevant. In Hex, you can use range angles to focus the docking search around a selected starting orientation.
This is useful when you want to make a docking run more targeted, but it comes with an important trade-off: a restricted search can exclude a plausible pose if your starting orientation is poor. The goal is not simply to make the search as narrow as possible. It is to use what you know about the system to set a sensible search region.
Prepare the structures before narrowing the search
Start with a receptor and a ligand. If you are using your own structures, clean and protonate them before docking. The SAMSON preparation workflow can remove atoms with alternate locations, remove waters and other unwanted components, and add hydrogens when they are missing. If a protein has missing residues or heavy atoms, the PDBFixer extension can be used to help fix it.
Preparation matters because docking results are only as useful as the structures you give the search. At the same time, don’t change hydrogens that were already added using a chosen protonation state. If you want to follow the tutorial’s example, its sample document contains two proteins, 2PTC_E and 2PTC_I.
Use the starting pose to define the search region
Open Hex in SAMSON, set one protein as the receptor and the other as the ligand, and choose Range angles as the sampling method. In Hex, the search domain is defined using spherical coordinates around the intermolecular axis connecting the centers of the proteins. A range angle of 180 degrees means there is no angular restriction; a smaller value limits the orientations considered to a cone around the starting direction.
If you already know where the binding site is, first move and orient the ligand near that site. You can use a Move editor in SAMSON to translate and rotate it. Then set the receptor and ligand range angles in Advanced parameters. The tutorial uses 45 degrees for each as an example of a constrained search. This is a starting point, not a universal setting: choose restrictions that reflect how much confidence you have in the initial placement and the likely interface.
You can also limit the ligand’s twist rotation about the intermolecular axis. These controls help focus sampling, but they do not establish that the chosen orientation is biologically correct. If the binding site is unknown, or the initial pose is uncertain, broadening the search may be more appropriate than imposing tight angular limits.
Balance search detail with run time
Hex can use a low-resolution Steric scan to screen orientations before a higher-resolution Final search. The first phase covers the search space coarsely; the final phase evaluates the retained candidates more finely. The documentation notes that a Steric scan order of 16–18 is often sufficient, and describes combinations such as N=16 for the scan and N=25 for the final search as practical starting points.
The Final search order controls the 3D expansion order. The default, N=25, is usually sufficient for many purposes. The documentation suggests N=30 for high-resolution crystal structures where binding-related conformational changes are expected to be small, and N=25 for model-built or more flexible structures. Higher-detail calculations can take longer, so it is worth matching settings to the structures and question at hand rather than automatically choosing the largest search.
Interpret poses as candidates, not conclusions
After docking, inspect the Results tab. Hex groups modes into clusters, and you can view the best-scoring mode per cluster or all modes. Selecting a row restores the corresponding ligand conformation; you can also create a conformation in the document from a result. Comparing clusters and inspecting several promising poses can help you understand whether the search produced recurring arrangements or a range of alternatives.
Before choosing candidates for further modeling, examine them with visual models, measurements, or interaction analysis. SAMSON’s Protein-Ligand Interaction Analyzer can compute contact area, hydrogen bonds, and surrounding residues. The Hydrogen Bond Finder can help visualize hydrogen bonds between the ligand and receptor. These analyses provide additional ways to inspect a pose; they do not replace careful scientific judgment.
The practical takeaway: use a focused search when you have evidence to guide it, preserve a starting conformation if you may want to repeat the run, and inspect the resulting poses before treating any one of them as a candidate worth pursuing.
Learn more in the Protein docking with Hex tutorial.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.