A docking or simulation workflow can be ready to run while its protein structure is not. Alternate atom positions, missing atoms, unwanted molecules, or incomplete residues can complicate preparation and affect downstream modeling. The tricky part is that “cleaning” is not one universal operation: removing a water molecule or ligand may be appropriate for one task and undesirable for another.
A useful approach is to separate protein preparation into two questions: What should be removed or standardized for this workflow? And what is actually missing or structurally problematic? SAMSON provides quick preparation tools for common cleanup, validation tools for inspection, and PDBFixer for deeper repairs.
Start with the workflow, not the cleanup button
Before changing a structure, consider what the next step needs. A docking setup, a molecular dynamics system, and a structure-analysis task may treat waters, cofactors, ions, and ligands differently. For example, SAMSON’s one-click preparation can delete ligands, cofactors, other small molecules, waters, and monatomic ions. Those options are convenient, but they should match the purpose of the model. Keep a copy of the input structure so you can revisit choices if needed.
If the structure looks complete and you mainly need routine cleanup, use Home > Prepare. It can remove alternate locations, delete selected categories of molecules, strip water, clear monatomic ions, and add hydrogens. This is a quick starting point—not a substitute for checking whether the resulting structure is suitable for your specific workflow.
Resolve alternate locations deliberately
Some structures contain alternative positions for atoms. Keeping all alternatives can leave a model with multiple positions for the same atom, while choosing one position simplifies the structure. SAMSON keeps the highest-occupancy atoms. If occupancies are tied or absent, it prefers alternate location A when available, then B, and so on.
To inspect the choices rather than simply applying a general cleanup, open Home > Validate, select the Alt. locations tab, and click Find alternate locations. Review the list, then use Remove alt. locations. This is especially useful when you want to know which parts of the structure contain alternatives before proceeding.
Check what a quick cleanup cannot repair
Removing unwanted molecules and adding hydrogens does not fill in missing residues or missing heavy atoms. The Structure Validation module can help identify other issues, including bond lengths outside expected ranges, non-standard residue aliases, and steric clashes. It also includes tools to merge nodes, reorder atoms in a connected component, and renumber atom serial numbers—useful housekeeping when preparing atom and node lists for simulations.
For side-chain clashes, the documentation points to SAMSON’s Rotamers editor, which can change side chains using a backbone-dependent rotamer library. Validation is therefore more than a final pass: it helps distinguish a structure that needs routine cleanup from one that needs a targeted repair.
Use PDBFixer when the structure is incomplete
If residues or atoms are missing, use the PDBFixer extension for a deeper repair. It can add missing residues based on SEQRES records, build missing heavy atoms and side chains, convert non-standard residues to standard equivalents, and add hydrogens for a specified pH. It can also remove water or heterogens, resolve alternate locations, build explicit-solvent water boxes with specified ions, and build lipid membranes around membrane proteins.
Hydrogen addition depends on the route you choose. Edit > Add hydrogens adds standard hydrogens at pH 7 for standard amino and nucleic acid residues, and uses valences for other structures. For pH-specific protonation, use PDBFixer. Whether to minimize after adding hydrogens depends on the downstream task; the documentation notes that AutoDock Vina needs only polar hydrogens for determining hydrogen bonds.
A simple decision path
- Mostly complete structure? Use Home > Prepare for the cleanup options that fit your workflow.
- Unsure what needs attention? Inspect alternate locations, bond lengths, non-standard residues, and clashes in Home > Validate.
- Missing residues or atoms, or need pH-specific hydrogens? Use PDBFixer and review the repair options relevant to your system.
- Preparing many structures? Batch Protein Prepare can process files in a folder or download structures from PDB identifiers and apply the same cleaning steps as Home > Prepare.
The goal is not to make every protein look identical. It is to make informed, task-appropriate changes, then check that the structure contains what the next step requires. For the complete walkthrough and interface details, read the protein preparation and validation tutorial.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.