If you’ve ever tried protein-protein docking and encountered strange results — unexpected clashes, misaligned complexes, or long computation times — chances are your system wasn’t properly prepared. Protein preparation is foundational for successful docking, yet it’s often overlooked or done inconsistently.
In this post, we’ll walk through how to clean up your protein structure before docking using the Hex Extension in SAMSON. Whether you’re new to molecular modeling or an experienced user, revisiting preparation best practices can save you hours of troubleshooting later on.
Why prepare your protein structure?
Crystal structures from the PDB often contain extraneous data such as water molecules, ions, or ligands — all of which can interfere with docking algorithms. Moreover, missing atoms, alternate locations, or an absence of hydrogens can lead to unrealistic interactions or outright docking failures.
Proper preparation includes:
- Removing alternate atom positions
- Removing water molecules, ions, ligands
- Adding hydrogen atoms, including pH-dependent ones
All-in-one preparation in SAMSON
SAMSON provides a simple, guided interface for structure preparation. Once your protein document is loaded, go to Home > Prepare and select the options for:
- Remove alternate locations
- Remove water, ligands, ions
- Add hydrogens
This single dialog lets you batch-process your cleanup with minimal effort. Here’s what the interface looks like:
Even better, SAMSON’s built-in visualization helps you verify that your structure has been cleaned, and the hydrogens are in place. You can also visually toggle atomistic and ribbon models in the Document view.
Fixing missing residues and atoms
If your system contains missing residues or incomplete side chains, you can use the PDBFixer extension. It allows you to:
- Repair side chains
- Add residues where needed
- Add hydrogens for a given target pH
This step is strongly recommended if the integrity of your structure is in doubt. Inconsistent or partial residues may not be visible at first glance but can negatively influence docking search and scoring.
Visual help during preparation
Tip: If the protein’s secondary structures (ribbons) are not visible, select the protein in the Document view and go to Visualization > Visual model > Ribbons. This adds clarity when checking the topology post-preparation.
You can also toggle atomic models on and off directly by using checkboxes in the Document view.
Best practices
- Always start from clean input structures.
- Save intermediate versions if you plan to test different docking parameters.
- If your protocol depends on specific protonation states or binding site orientations, do not use automatic hydrogen addition — customize with PDBFixer instead.
Fortunately, the tutorial file provided with the Hex guide already includes a clean system with hydrogens added and water removed, so it’s a good reference model.
To learn more, head over to the full tutorial on Protein docking with Hex.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download it at https://www.samson-connect.net.