If you’ve ever tried to prepare multiple protein structures for simulations or drug screening, you already know the struggle: inconsistent files, missing atoms, alternate locations, unwanted water molecules and ligands. Doing this manually for each structure is both tedious and prone to error.
This is where the Batch Protein Prepare extension in SAMSON can save time and maintain consistency across datasets. It’s especially useful for molecular modelers working with lists of structures identified by PDB codes, directories full of downloaded data, or custom-built molecular models.
Why Batch Preparation Matters
Clean, validated input structures are essential before starting any molecular design workflow like docking or molecular dynamics. Minor issues—such as ambiguous locations or missing atoms—can cause unexpected crashes or yield misleading results. Batch processing ensures all your structures are uniformly prepared without manual intervention.
What You Can Do with Batch Protein Prepare
SAMSON’s Batch Protein Prepare performs the same cleaning steps available through the single-step preparation tool under Home > Prepare, but for multiple files:
- Automatically download structures by PDB ID or prepare your local files
- Support for multiple formats: PDB, PDBx/mmCIF, MMTF, MOL2
- Preserve folder structure in output data for better organization
- Remove ligands, water, and ions that are not needed
- Add missing hydrogens based on residue and valences
Whether you’re preparing 10 or 1000 PDB structures, this tool will handle them all consistently. If PDB IDs are your starting point, you can supply them either as a list in a text file or enter them directly as a string.
Getting Started
Start by installing the extension from this page. You’ll find a user interface that lets you:
- Select a folder of structures to clean
- Specify which steps to perform (keep or remove ligands, ions, etc.)
- Choose whether to minimize or assign hydrogens by residue type or valence
Who Is This For?
This tool is built for researchers needing to pre-process large datasets before running binding energy calculations, protein-ligand docking studies, or building simulation systems. It is especially convenient for graduate students, structural biologists, computational chemists, and software developers creating molecular workflows.
In sum, Batch Protein Prepare reduces manual labor and helps ensure that your input data is clean, organized, and simulation-ready. It’s a small step that can save hours.
Learn more about protein preparation in SAMSON.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON from https://www.samson-connect.net.