Getting a protein ready for docking is often more time-consuming than the docking itself. Whether you’re preparing for virtual screening or structural analysis of complexes, the cleanup step is crucial. Missing hydrogens, alternate atom positions, leftover water molecules—these details can derail a well-intended docking task. The good news? In SAMSON, there’s a way to simplify it all.
Let’s take a look at how you can harmonize and sanitize your protein models in one step—using the integrated preprocessing tools in SAMSON, particularly handy when using the Hex Extension for protein-protein docking.
Common preparation pitfalls
- Incomplete side chains (missing heavy atoms)
- Alternate locations for atoms (e.g., “A” and “B” positions in PDB files)
- Unnecessary water molecules or ligands that skew docking results
- Inconsistent hydrogenation or irregular protonation
Pre-docking preparation is where many modeling workflows lose robustness and reproducibility. Often, this is managed through a combination of scripts, secondary software, or manual interventions in visualization tools.
How SAMSON simplifies the process
SAMSON provides a built-in interface under the menu: Home > Prepare, designed to perform all these tedious checks and corrections. Instead of jumping through hoops, simply check the appropriate boxes to:
- Remove atoms with alternate locations
- Remove water, ions, ligands
- Add missing hydrogens
This not only saves time but ensures consistency across different protein selections.
What if my protein has missing atoms?
If your structure is even more complex—say it has incomplete residues or unresolved electron densities—you can use the PDBFixer extension in SAMSON to repair proteins.
This extension lets you fill missing heavy atoms, reconstruct loops, and even adjust protonation according to the desired pH. It’s a good practice to integrate this step before hydrogenation, especially if you work with modeled or experimental structures with gaps.
For visual clarity
Another perk is the tight connection between system preparation and visualization. After cleanup, you can improve interpretation by switching on Visual model > Ribbons under Visualization. This helps you better understand the structural context of your docking inputs, including secondary elements or flexible regions.
Bottom line
If you’re tired of bouncing between preprocessing tools just to get your proteins into shape before protein-protein docking, give SAMSON’s preparation workflow a try. Whether you are setting up a cryo-EM fit, a crystal structure refinement, or a machine learning pipeline requiring harmonized input features—the one-click preparation within SAMSON gets your molecules ready reliably and quickly.
To learn more, consult the full documentation for Protein docking with Hex in SAMSON.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.