Have you ever run a protein-ligand docking simulation, only to find that the ligand doesn’t bind correctly—or worse, doesn’t bind at all? 🤯 Before diving into docking parameters or refining your scoring function, consider this: the problem might lie in your protein structure itself.
In fact, one of the most overlooked steps in molecular docking is protein preparation. Incorrect bond orders, missing hydrogens, alternate atom locations—these can all derail even the most carefully planned simulations. The FITTED Suite Extension in SAMSON simplifies this process by wrapping several preparatory tools, but it’s still essential to understand what the software is doing under the hood—and why it matters.
Common pitfalls during protein preparation
- Missing or misplaced hydrogen atoms: Hydrogen bonding patterns are often critical for accurate docking. Even one misplaced hydrogen can change docking outcomes significantly.
- Alternate conformations: Many PDB files contain multiple locations for certain atoms. These need to be resolved to avoid confusion during ligand binding.
- Water molecules: Some water molecules are essential, while others just get in the way. Deciding which to remove is critical.
- Incorrect bond orders: Especially relevant for ligands bound covalently to receptors, improper bond orders can lead to erroneous poses or failed simulations.
A closer look at FITTED’s PREPARE tool
When using the FITTED Suite inside SAMSON, protein preparation is automated through a tool called PREPARE (Protein Rotamers Evaluation and Protonation based on Accurate Residue Energy).
PREPARE handles:
- Bond order correction
- Hydrogen addition
- Tautomer generation
- Hydrogen bond network optimization
It uses an iterative algorithm to optimize hydrogen positioning, improving the accuracy of resulting docked poses.
Best practices before docking
Before you launch into your docking run, take just a few minutes to:
- Inspect the protein file for alternate atom locations. In SAMSON, this is easy with the Document view panel.
- Use Home > Prepare if you’re making manual decisions about which atoms or waters to remove.
- If you’re unsure whether everything is fine, allow PREPARE to handle it—but keep an eye on the output logs and final structures.
Skipping this step can lead to unreliable docking results, wasted computation time, and incorrect biological conclusions.
Efficiency without compromise
For users working with covalently bound ligands, FITTED goes a step further: allowing you to manually define hybridization states and bond orders when needed. This additional control is useful in more complex systems, such as metalloproteins or covalent inhibitors.
Final thoughts
While SAMSON’s FITTED Suite reduces the number of manual steps required, an informed user is still the best operator. Understanding protein preparation not only improves your results but saves you time down the line by avoiding common errors.
To learn more details and go through an example step-by-step, visit the full documentation page on the FITTED Suite: https://documentation.samson-connect.net/tutorials/fitted/fitted-suite/.
SAMSON and all SAMSON Extensions are free for non-commercial use. Get your copy at https://www.samson-connect.net.