If you’ve ever had to prepare multiple protein structures for docking, simulations, or other modeling tasks, you know how tedious and error-prone it can become. Opening each file, fixing alternate atom locations, removing waters or cofactors, checking for missing atoms—it’s easy to lose hours, especially when you’re working with a dataset of tens or even hundreds of PDB codes. Fortunately, SAMSON’s Batch Protein Prepare extension can do the heavy lifting for you.
Whether you’re screening drug candidates or running large-scale simulations, cleaning your protein structures is critical. Structural issues can cause crashes or artifacts downstream, so it’s important to get things right from the start. But cleaning structures manually one by one doesn’t scale well. This is where batch preparation can really help.
The Problem: Structural Cleanup at Scale
Molecular databases often contain structures that are not simulation-ready: missing atoms, alternate locations, solvent residues, non-standard ligands, etc. For high-throughput scenarios, manually addressing these issues is not just frustrating—it’s inefficient and prone to inconsistency.
The Solution: Batch Protein Prepare
The Batch Protein Prepare extension in SAMSON makes bulk cleanup easy. It automates the standard cleaning steps used in the Home > Prepare menu, but applies them across multiple files or PDB codes with only a few clicks. Here’s what it can do:
- Prepare structures in a folder: Automatically processes PDB, PDBx/mmCIF, MMTF, and MOL2 files. Maintains your original subfolder structure, so output stays organized.
- Download and prepare by PDB IDs: Provide a list or string of PDB codes, and it will fetch, clean, and save them—no need to download or organize files manually beforehand.
The cleaning steps include removing alternate locations (based on atom occupancy), deleting ligands and non-essential molecules, stripping waters and monatomic ions, and adding hydrogens as needed. Each file ends up ready for simulation software like GROMACS or docking tools like AutoDock Vina.
How to Use It
Once installed from SAMSON Connect:
- Launch the Batch Protein Prepare extension.
- Select files from a folder—or paste in your PDB codes.
- Choose your cleanup options (or go with default settings).
- Click ‘Run’, and let the extension handle the rest.
It’s especially helpful when paired with other SAMSON tools like the PDBFixer extension (for deeper structural repair) or the Rotamers Editor (for resolving side-chain clashes).
Why It Matters
Having a clean, consistent workflow is not just convenient—it helps maintain reproducibility in your research. Instead of spending time on file-by-file maintenance, batch preparation lets you spend time analyzing results and building insights.
To learn more about the full SAMSON protein preparation workflow, visit the official documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.