Anyone working with molecular models knows the slow drip of time lost to repetitive cleanup tasks: removing waters, deleting unwanted ligands, fixing missing atoms, and ensuring the structure won’t crash a simulation. It’s manageable when working with one or two files. But what happens when you’re handling dozens—sometimes hundreds—of PDBs?
That’s where Batch Protein Prepare in SAMSON can help. Whether you’re screening a library for ligand binding or preparing multiple systems for molecular dynamics simulations, this feature smooths out the whole process.
Why Batch Preparation Matters
In protein modeling workflows—especially high-throughput ones—it’s not just about having the data. It’s about having the data ready. A poorly prepared protein model can introduce artifacts, trigger simulation errors, or mislead interpretation.
When you’re processing multiple proteins, manual cleanup just isn’t practical. Manually opening, editing, and saving each structure multiplies the chances of inconsistencies and slows research down. Batch Protein Prepare automates the cleanup, ensuring consistency across all your files.
What Batch Protein Prepare Does
This SAMSON Extension provides automation for the following tasks:
- Automatically downloads structures based on PDB identifiers
- Removes alternate locations with ambiguous atom positions
- Deletes unnecessary ligands, including covalently attached ones
- Strips water molecules and monatomic ions
- Adds missing hydrogens based on residue type
The output mimics what you’d get using the Home > Prepare dialog, but it can be applied to an entire folder full of structures in formats like PDB, mmCIF, MMTF, or MOL2. You don’t even need all the PDB files beforehand—just input their identifiers and let the tool fetch and clean them for you.
Supported Workflows
Batch Protein Prepare is particularly useful in the following scenarios:
- Virtual screening: Preparing receptors before docking libraries of ligands.
- Comparative modeling: Ensuring consistency across a set of homologous proteins.
- Time-limited projects: Accelerating preparation for teaching, presentations, or demos.
Because the extension preserves subfolders during output, it’s also easy to keep everything organized—which matters when you’re juggling complex datasets.
How It Works
To get started, install the Batch Protein Prepare extension from SAMSON Connect. Once installed:
- Specify the folder of PDB files, or enter a list of PDB identifiers.
- Choose the preparation steps to apply (or use defaults).
- Run the process — the extension will clean, protonate, and save your structures automatically.
Conclusion
Manual structure prep doesn’t scale. If you often work with sets of protein structures, take advantage of SAMSON’s Batch Protein Prepare extension. It reduces tedious steps, lowers the risk of human error, and gets your models ready for downstream simulation or analysis in no time.
Learn more about preparing and validating proteins in SAMSON
SAMSON and all SAMSON Extensions are free for non-commercial use. Try it out or download it today at https://www.samson-connect.net.