If you’ve ever docked a ligand into a protein structure and wondered why the results weren’t quite what you expected, you’re not alone. One of the most frequent—and easily overlooked—issues in molecular docking is whether to perform protein structure preparation before running your docking simulations. So, what should you actually do?
In this post, we’ll explore a practical scenario using SAMSON and the FITTED Suite Extension to clarify when protein preparation is necessary—and when it’s not. By diving into how FITTED Suite automates protein preparation, we aim to help modelers avoid redundant or conflicting preprocessing steps that could degrade results rather than improve them.
Preparation: Automated, But With Limits
The FITTED Suite handled in SAMSON includes a built-in tool called PREPARE, which automatically performs several preprocessing steps on your protein structure:
- Adjusting bond orders
- Adding hydrogens
- Generating possible tautomers
- Optimizing the hydrogen bonding network
- Dealing with water molecules as needed
In many cases, that’s all you need. When running tutorials like the one with 1E2K (non-covalent docking) or 5MAJ (covalent docking), the system is already formatted correctly, and FITTED Suite takes care of the rest.
So what’s the catch? If your protein structure includes complex issues such as alternate atom locations, missing residues, or incorrectly modeled side chains, you might need to intervene.
When Should You Step In?
While FITTED Suite handles much of the dirty work, here are some specific cases where you may want to—or need to—do additional cleaning:
- Alternate locations: If your PDB file includes multiple conformations for the same atom, remove them unless you have a specific reason to include both. In SAMSON, this can be done easily using Home > Prepare.
- Missing atoms or residues: If parts of your protein are incomplete, any derived grid or electrostatic setup might be flawed. Check out SAMSON’s Protein Preparation & Validation guide for how to fix these issues.
- Non-standard residues or ligands: Verify that these have correct bond orders and valency. Use the Inspector in SAMSON to validate or edit properties like hybridization explicitly.
Are You Over-Preparing?
A common mistake is to preprocess everything—minimize, protonate, remove waters—before loading into SAMSON. But this may interfere with the automated PREPARE step in FITTED Suite, leading to inconsistent results. Trust the automation when it’s designed for it, and carefully assess which parts are really needed in your case.
What If You’re Not Sure?
When in doubt, load your structure as-is and let PREPARE handle it. Then inspect the resulting processed protein in the Document view. If it looks correct, you’re good to go. If something seems off, such as strange hydrogen bonding or valency issues, then consider manual intervention.
Here’s what the Document View might look like after the receptor is processed:
Final Tip
Next time you prepare a protein for docking, pause before running an external minimization or water deletion. It could be that SAMSON and the FITTED Suite already have you covered — automatically and reproducibly.
Want to explore more capabilities and see FITTED Suite in action? Learn more here.
SAMSON and all SAMSON Extensions are free for non-commercial use. Try it out by downloading SAMSON directly at https://www.samson-connect.net.