If you’ve ever handled multiple PDB files, you know the pain of preparing them one at a time before a molecular modeling workflow. Manually opening each structure, checking for alternate locations, removing waters or ions, and adding hydrogens can easily turn into hours of repetitive work.
This is a common bottleneck for molecular modelers working with libraries of protein structures for virtual screening, molecular dynamics, or other simulations. Fortunately, there’s a very efficient way to streamline the entire process using SAMSON and its extension Batch Protein Prepare.
What is Batch Protein Prepare?
Batch Protein Prepare is an extension for the SAMSON molecular design platform that automates the protein cleaning and preparation process. Whether you have a folder full of structures or just a list of PDB codes, this tool helps you prepare everything using the same well-defined pipeline.
What It Does
- Prepares structures in supported formats:
.pdb,.cif/mmCIF,.mmtf,.mol2. - Downloads structures automatically from the PDB if you don’t already have the files.
- Applies the same cleanup steps as Home > Prepare for each file:
- Removes alternate locations (keeps highest occupancy).
- Strips water molecules, ions, and unwanted ligands.
- Adds hydrogens based on residue type or valence.
- Preserves the subfolder structure of the input folder in the output folder, making it easier to manage large datasets.
This saves time, reduces errors, and ensures consistency across all your input structures.
When Should You Use It?
If you’re working with any of the following tasks, Batch Protein Prepare is probably useful:
- High-throughput docking where each protein variant or target has to be ready for AutoDock Vina or similar tools.
- Batch molecular dynamics simulations where correctly prepared protein structures are critical to avoid runtime crashes.
- Preparing a dataset for machine learning applications based on protein-ligand or structure-based features.
It’s especially handy in workflows where you download multiple structures from the PDB and want to clean them all in one go. You can simply provide a list of PDB codes in a text file, and SAMSON handles downloading and preparation automatically.
How It Looks
To Try It Yourself
1. Download the extension from here.
2. Open SAMSON and access the Batch Prepare tool.
3. Choose a folder or input PDB identifiers.
4. Set any preferences and run the preparation.
That’s it — you’ll get clean, prepared structures ready for simulation or modeling tasks, with consistent processing and without file-by-file handling.
For more details, 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 download SAMSON at https://www.samson-connect.net.