If you’ve ever tried to prepare dozens or even hundreds of protein structures for simulations or machine learning, you know how quickly things can become tedious. Downloading PDB files, stripping water and ions, resolving alternate locations, adding missing atoms… And that’s just before you validate if the structure is even suitable for downstream work.
Whether you’re curating a dataset for training models or prepping for a high-throughput screening, the repetition of “cleaning” protein files is a common frustration. Fortunately, there’s a way to significantly reduce this heavy lifting using SAMSON’s Batch Protein Prepare extension.
Why Batch Preparation Matters
Protein structures from the Protein Data Bank (PDB) often contain unnecessary molecules like water, ligands, or ions not needed for your workflow. They might have missing atoms or ambiguous alternate locations. Left as-is, these issues can derail simulations and reduce the quality of your results.
Fixing these problems manually across hundreds of files is time-consuming. The Batch Protein Prepare extension for SAMSON automates this process, saving attention for the more interesting parts of your research.
How It Works
The extension allows you to prepare a folder full of protein structures at once. It applies the same proven cleaning logic as you would use via SAMSON’s Home > Prepare button, including:
- Removing alternate atom locations, keeping the highest-occupancy positions.
- Deleting unnecessary ligands and monatomic ions.
- Stripping water molecules.
- Adding missing hydrogen atoms intelligently.
But the real win comes when you realize it can also fetch and prepare structures from the PDB for you. Just give it a list of PDB identifiers—either in a text file or as a comma-separated string—and it handles the downloads, cleanup, and organization.
Supported Formats and Features
The extension supports common file formats used in structural biology and cheminformatics, such as:
.pdb.mmCIF/.pdbx.mmtf.mol2
It preserves folder structures and names in the prepared output, making it easier to track and document your datasets.
A Visual Walkthrough
The interface is straightforward. Just point it to a folder, select preparation options, and run the batch. The visual preview and logs keep you informed without overwhelming you with details.
Who Benefits Most?
This tool is especially useful if you:
- Need to clean large public datasets before modeling.
- Want to run molecular docking simulations across multiple proteins.
- Work in structural bioinformatics or data-driven drug design.
- Teach or coordinate workshops where multiple prepared structures are needed.
Conclusion
Protein preparation doesn’t have to be a bottleneck. With the Batch Protein Prepare extension in SAMSON, you can automate tedious structure cleanup and get back to focusing on what matters—designing and analyzing molecules.
To learn more, visit the full documentation page 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.