Anyone who has worked with protein structures knows that small structural issues can lead to big problems down the road. Whether you’re docking ligands, running molecular dynamics simulations, or building models for drug screening, structure validation is what stands between a productive workflow and a simulation crash.
But here’s the good news: validating a protein system in SAMSON is not just thorough—it’s also user-friendly.
Why Validation Before Simulation Matters
You might be tempted to jump straight into your main molecular modeling tasks. However, a few overlooked problems in your input structure—like alternate atom locations, unrealistic bond lengths, or unrecognized residues—can compromise results or waste hours of compute time.
SAMSON offers a streamlined process to catch and fix these issues early. This blog post walks you through the validation tools available under Home > Validate.
Common Issues You Can Catch Early
SAMSON’s Structure Validation module is designed to help you:
- Remove alternate locations: These occur when atoms have multiple positions recorded. SAMSON keeps the highest-occupancy atoms, following a sensible fallback strategy using alt-loc codes like A, B, etc.
- Review bond lengths: Unusual bond lengths could be signs of poor structure quality or missing atoms.
- Identify non-standard residues: SAMSON attempts to interpret known aliases, but it also flags residues that might need user clarification.
- Detect steric clashes: Visualize contacts that may lead to energy spikes and see where side chains might be too close to each other.
Make It Clean: Fix What You Find
Once issues are identified, SAMSON makes it easy to clean up:
- Resolve alternate locations with a single click.
- Use the rotamer editor to adjust side chains in case of clashes. This tool utilizes a backbone-dependent rotamer library to provide chemically reasonable configurations.
- Reorder and renumber atoms to suit your simulation software’s requirements. These options help ensure your atom lists are contiguous and logically organized.
- Merge nearby nodes if your model has been edited and could benefit from consolidation.
When to Use This
Consider this step a standard part of preparing any newly imported structure, especially if you’re using structures downloaded from the Protein Data Bank (PDB) or built by homology modeling. Even a “quick check” might spare you a failed simulation hours later.
Automate the Basics, Dive Deeper When Needed
Of course, you can prepare a protein in one click using Home > Prepare. But when you’re working on mission-critical models—or puzzled why a simulation fails—the validation tools in SAMSON provide the control you need.
Want to dig deeper into protein preparation and validation in SAMSON? Visit the full documentation here: https://documentation.samson-connect.net/tutorials/prepare-protein/prepare-protein/.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.