Anyone who’s worked with protein structures knows the routine: download a dozen PDB files, clean each one manually, and try not to make mistakes along the way. It’s tedious—and it’s easy to overlook a missing hydrogen or a dangling ion.
If you’ve ever thought, “There must be a better way,” you’re not alone. Automating protein preparation is not only convenient—it helps ensure consistency and reproducibility across your simulations and analyses.
Why Batch Protein Preparation Matters
Preparing one protein model is manageable. But cleaning 50—or 500? That’s another story. Manual errors quickly accumulate, and inconsistencies between structures can lead to unreliable results in molecular dynamics, docking, or any downstream bio-computational study.
That’s where the Batch Protein Prepare extension in SAMSON comes in. It gives you an automated, standardized way to pre-process many structures at once—saving time and reducing errors.
What You Can Do With It
This SAMSON Extension applies the same structure-cleaning workflow available via Home > Prepare, but at scale. Here’s what it can handle:
- Batch process local files in PDB, mmCIF (PDBx), MMTF, or MOL2 format.
- Download and prepare structures directly by supplying PDB IDs (typed as a string or loaded from a file).
- Preserve folder structure in outputs, so your projects remain tidy and traceable.
Typical preparation actions include:
- Removing alternate atom locations (keeping highest-occupancy atoms).
- Deleting ligands, co-factors, monatomic ions, and water molecules.
- Adding hydrogens as needed, based on standard valence or residue information.
When Should You Use It?
If you’re preparing a dataset for virtual screening, machine learning, or any large-scale structural analysis, Batch Protein Prepare streamlines your workflow. It’s especially helpful when:
- You want consistent preprocessing across a dataset.
- You’re working with representative structures from a protein family.
- You want to extend an existing pipeline with reproducible cleaning steps.
How to Get Started
1. Install the Batch Protein Prepare extension from SAMSON Connect.
2. Load your folder of structures or list of PDB codes.
3. Select output preferences and click prepare.
That’s it. Your cleaned, ready-for-analysis structures will be saved automatically.
Conclusion
Protein preparation is too important to leave to error-prone manual work—especially when you’re dealing with many files. With SAMSON’s Batch Protein Prepare, you can clean entire datasets in a few clicks, helping you move faster and more confidently toward analysis.
Learn more in the documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.