If you work with protein-ligand docking, molecular dynamics, or virtual screening, you’ve probably faced the time-consuming chore of preparing dozens—or hundreds—of protein structures. From removing unwanted molecules to adding missing atoms, the process can quickly become a bottleneck.
That’s where Batch Protein Prepare in SAMSON comes in. If you need to clean a collection of structures for simulations or screening campaigns, this tool automates much of the manual effort, preserving consistency across datasets and saving hours of work.
Why batch preparation matters
Modern pipelines often begin with a list of PDB codes or a folder full of downloaded protein structures. But raw files from the Protein Data Bank may include alternate locations, water molecules, ions, co-factors, and even missing atoms or residues. Ignoring these issues risks flawed simulations or unexpected failures later in the workflow.
Batch preparation lets you:
- Quickly apply consistent cleaning steps to multiple files
- Download PDB structures directly using their identifiers
- Retain folder structures for organized output
- Save processing time compared to doing everything manually
What you can clean in a batch
Using the Batch Protein Prepare extension in SAMSON, you can process structures in several formats—including PDB, mmCIF, MMTF, and MOL2. Simply choose a directory containing your input files (or a PDB code list), and the extension lets you:
- Remove alternate locations (keeping only the most likely conformers)
- Delete ligands, water molecules, and monatomic ions
- Add missing hydrogens depending on residue type or valence
These are the same steps you would go through manually under Home > Prepare in SAMSON—but applied automatically across your dataset.
Use case: Preparing a library for virtual screening
Imagine you’re about to run docking simulations across a diverse set of targets. You’ve collected 50 PDB files from different studies. Running these through the Batch Protein Prepare tool lets you:
- Ensure a uniform preparation protocol across the dataset
- Eliminate human errors from manual structure editing
- Streamline downstream steps like docking and scoring
Get started in minutes
If you already use SAMSON, installing the Batch Protein Prepare extension only takes a click. Once activated, you’ll find it under your installed extensions. Point it to your folder, set your output path, and customize your cleaning preferences. SAMSON will process each structure, replicate the directory tree if needed, and save the cleaned versions—all without you opening a single file manually.
To learn more and see the full range of protein preparation tools in SAMSON, visit the official documentation: https://documentation.samson-connect.net/tutorials/prepare-protein/prepare-protein/.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.