A protein–protein docking run can produce a long list of plausible-looking poses—and still leave you unsure where to start. Searching every possible orientation is expensive, while narrowing the search too aggressively can exclude a useful pose. The practical challenge is to use what you already know about the binding site to focus the calculation, then inspect the results with appropriate care.
The Hex extension in SAMSON offers a way to manage that trade-off: define a starting arrangement, constrain the rotational search with range angles, and use a coarse-to-fine search. These choices can make a docking workflow more focused without turning a predicted pose into experimental evidence.
Start with structures you can trust
Before configuring the search, prepare the receptor and ligand. The tutorial’s sample contains two protein models, 2PTC_E and 2PTC_I, but you can load your own structures. Remove alternate-location atoms, water, monatomic ions, and ligands when appropriate, and add hydrogens if they are missing. If a protein has missing residues or heavy atoms, the PDBFixer extension can help address those gaps. Avoid changing hydrogens when they already reflect a protonation setup you intend to preserve.
Open Hex via Home > Apps > Biology > Hex. Set one protein as the receptor and the other as the ligand. Saving the ligand’s initial conformation before docking is useful if you later want to repeat the calculation with different settings while keeping the starting conformation consistent.
Use prior knowledge to focus the search
Hex performs its rotational docking search in spherical coordinates. With the Range angles sampling method, receptor and ligand orientations can be restricted to cones around the intermolecular axis connecting the protein origins. A range of 180 degrees means no angular restriction; a smaller value limits the orientations considered.
If the likely binding region is known, first move and orient the ligand near that site. Then set the receptor and ligand range angles in Advanced parameters. The tutorial demonstrates 45 degrees for each. Think of that as an example starting point, not a universal setting: the narrower the range, the more important it is that the starting arrangement points toward the relevant interface. If the binding site is uncertain, a tight constraint could leave out useful orientations, so a broader search may be more appropriate.
You can also limit the ligand’s twist rotation about the intermolecular axis. These constraints are most useful when they encode real structural knowledge—for example, known interface residues—not simply a desire to make the calculation finish sooner.
Let a coarse pass reduce the workload
Hex can run a low-resolution Steric scan before the higher-resolution Final search. The scan quickly evaluates orientations and retains a smaller set for the finer stage. The documentation notes that scan orders of 16–18 are sufficient in many cases and gives combinations such as N=16 for the Steric scan followed by N=25 for the Final search. A higher Final search order uses finer distance increments, but a full high-resolution calculation can take longer.
As a general starting point, the tutorial describes N=25 as usually sufficient, N=30 for high-resolution crystal structures when binding-related conformational changes are expected to be small, and N=25 for model-built or more flexible structures. Treat these as guidance rather than guarantees: the right settings depend on the structures and the question you are asking.
Correlation type and post-processing also affect what the results mean. Electrostatics may help when the proteins have complementary formal charges, but the tutorial advises against using it for DNA or RNA docking. A bumps counter can identify solutions with steric clashes. Molecular-mechanics refinement is described as alpha-stage and is most appropriate when conformational changes are expected to be small; it can eject ligands with incorrect conformations from the binding site.
Inspect poses instead of relying on a score alone
After clicking Run docking, review the clustered modes in the Results tab. Selecting a row restores that ligand conformation, and you can create a conformation in the document for further inspection. Check whether the interface is structurally plausible, look for clashes, and use interaction-analysis tools to examine contacts or hydrogen bonds. A ranking or an attractive pose is a candidate for further analysis—not, by itself, confirmation of a biological interaction.
For the full 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.