If you work with multiple protein structures, you know the pain of repetitive cleanup tasks: removing water molecules, fixing alternate locations, adding hydrogens… doing it dozens of times is tedious, error-prone, and slows down your workflow dramatically.
Luckily, if you’re using SAMSON, there’s a way to automate all of that. The Batch Protein Prepare extension makes it possible to clean dozens — even hundreds — of structures in one go. Whether you have a folder full of structures prepared in-house or you’re just starting from a list of PDB identifiers, Batch Protein Prepare has you covered.
What It Solves 🛠️
Let’s say you’re screening small molecules over multiple protein variants, or generating a benchmark set for machine learning. Usually, each structure requires the same set of preparation steps:
- Removing alternate atom locations
- Stripping water molecules
- Deleting ligands and irrelevant ions
- Adding hydrogens appropriately
Doing this manually for many files is frustrating, especially with slight inconsistencies between PDB records. Batch Protein Prepare lets you automate these steps.
Two Modes of Use
1. Preparing Existing Files
Have a collection of PDB, mmCIF, MMTF, or MOL2 files? Just point the Batch Protein Prepare extension to a folder. It will go through each file, apply the standard preparation steps from Home > Prepare, and write out the results — preserving the internal folder structure.
2. Downloading via PDB IDs
Don’t have the files locally? No problem. Provide a list of PDB identifiers (as a plain-text file or a string), and Batch Protein Prepare will download them automatically, apply all cleanup steps, and save the results.
This means you can go from a list like:
|
1 2 3 |
1CRN 6LU7 3CLN |
… to a cleaned, hydrogenated, simulation-ready dataset in just a few clicks.
Why It Matters
Clean structures are essential for any downstream task: docking, MD, structure-based drug design, free energy calculations — poor preprocessing introduces subtle errors, wasted time, or worse, incorrect conclusions. Doing it properly, consistently, and fast makes your work more robust and reproducible.
Get Started
To use Batch Protein Prepare in SAMSON:
- Install the Batch Protein Prepare extension.
- Launch the extension from SAMSON’s Extension menu.
- Choose whether you want to operate on local files or enter PDB codes to download.
- Run the batch job and watch your preprocessing disappear from your to-do list.
To learn more about protein preparation workflows in SAMSON, visit the full documentation here: SAMSON Protein Preparation Documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.