Anyone who has worked with multiple protein structures knows the challenge: each file needs cleanup before starting a molecular dynamics simulation, docking calculation, or structural analysis. Removing water, handling alternate locations, fixing missing hydrogens—it’s the sort of repetitive task that no scientist enjoys.
If you routinely work with protein structures from the PDB, the new Batch Protein Prepare extension in SAMSON offers a solution that can save hours of manual effort. Whether you are managing dozens—or even hundreds—of protein structures, this tool automates the preparation steps so that you can focus on your scientific questions, not file formatting.
Why It Matters
Most molecular workflows assume the input protein structures are clean and complete. But publicly available PDB structures often contain water molecules, co-factors irrelevant to your simulation, alternate locations, or missing atoms. These issues can affect downstream tasks such as docking accuracy, force-field assignment, or even simulation stability.
While these problems can be addressed manually, doing so for multiple structures quickly becomes labor-intensive. That’s where the Batch Protein Prepare extension steps in.
What It Does
The extension applies the same cleaning logic found in Home > Prepare but scaled to multiple files. Here’s what it handles automatically:
- Alternate atom locations — keeps only highest-occupancy atoms.
- Ligand removal — strips co-factors and covalently bound small molecules.
- Water and ions — removes solvent and monatomic ions.
- Adds hydrogens — default protonation at pH 7 for compatible residues.
Two Ways to Use It
You can either:
- Clean up existing files — point to a folder containing PDB, PDBx/mmCIF, MMTF, or MOL2 files. The tool will preserve the internal folder structure in its processed output.
- Download and prepare PDB structures directly — submit a list of PDB codes (as text or a string input). The extension will automatically download and prepare the structures.
Who Might Benefit
This tool is especially useful if you:
- Run high-throughput docking or MD simulations with multiple protein receptors.
- Are preparing datasets for training machine learning models on structural data.
- Just want to save time when inspecting experimental PDB structures.
Getting Started
To install the extension, search for Batch Protein Prepare from within the SAMSON Extension Store or click here. Once installed, you can access it from within the SAMSON interface and start batch-preparing structures with a few clicks.
This kind of automation can greatly reduce preparation bottlenecks and help ensure consistency across large datasets. Whether you’re cleaning ten structures or a thousand, this extension ensures each gets the same, reliable treatment.
💡 Tip: If you have more complex preparation needs (e.g., adding missing residues, converting non-standard residues), consider pairing this with the PDBFixer extension for deeper structure repair.
To learn more about all protein preparation tools in SAMSON, visit the full documentation: 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.