Preparing a single protein structure for simulations is already a multi-step process. If you’ve ever had to do that with dozens or hundreds of PDB files, you’ve probably felt the pain of repetitive cleanup: removing unwanted molecules, adding missing atoms or hydrogens, stripping water, and more.
Fortunately, SAMSON’s Batch Protein Prepare extension was built to streamline exactly this situation.
Why Batch Preparation Matters
Whether you’re performing virtual screening, molecular docking, or large-scale structure refinement, working with many PDB files often means you need to clean them with the exact same protocols. Doing it one-by-one is time-consuming and error-prone.
How Batch Protein Prepare Works
Batch Protein Prepare automates the protein preparation workflow across entire folders of files or based on lists of PDB IDs. It replicates the structural cleaning steps from SAMSON’s main Prepare functionality, including:
- Stripping water, ions, and unneeded ligands
- Removing alternate locations (keeps highest occupancy)
- Adding hydrogens based on residue types
You can use it in two primary ways:
- Prepare local structures: Point to a folder containing input files. These can be in
PDB,mmCIF,MMTF, orMOL2formats. Output keeps the original folder structure for consistency. - Download and prepare structures: Provide a list of PDB codes—either as a string or from a text file—and Batch Protein Prepare downloads them, prepares them, and saves the result.
When to Use Batch Protein Prepare
This extension becomes especially useful in workflows such as:
- Prepping a curated dataset of protein targets for benchmarking
- Downloading sets of homologous proteins for comparative studies
- Generating clean input files for machine learning or statistical modeling
It’s great for any context in which you want uniform preparation across many structures with minimal manual oversight.
Visual Walkthrough
The above interface lets you select input options, specify what to clean, and set the output directory. You don’t need scripting experience—everything is accessible through a visual interface.
Small Details That Make a Difference
A few thoughtful design choices make the extension even more helpful:
- It supports both legacy and extended PDB identifiers.
- If you already have cleaned structures, the extension won’t overwrite unless you tell it to.
- Outputs preserve folder hierarchies. This is great if downstream tools expect a mirrored structure.
A Time-Saver for Everyday Work
Instead of preparing each protein individually, use Batch Protein Prepare to get consistent, validated structures in just a few clicks. This frees you up to focus on design, simulation, or analysis—instead of cleanup.
Learn more from SAMSON’s official documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.