Preparing protein conformations properly is a necessary step before computing transition paths between them. However, it is often a source of frustration for molecular modelers. Missing atoms, inconsistent residue numbering, or incompatible PDB files can all lead to failed simulations or incorrect results.
In this post, we’ll walk through best practices to prepare two different conformations of a protein for use with the Protein Path Finder app in SAMSON, a platform for integrated molecular design. This applies to anyone working with experimental or modeled structural data aiming to analyze transitions between states—such as an enzyme shifting from open to closed conformations.
Why proper system preparation matters
The transition path search uses structural similarity and atomic mappings between conformations. This means both conformations must:
- Contain the same atoms, residues, and chains in the same order
- Share a consistent structure and atom naming
- Be minimized to remove steric clashes and prepare for energy-based search
Even small mismatches—such as a missing hydrogen or an extra ligand—can invalidate results or hinder pathfinding.
Merging conformations into one file
If your conformations are in separate PDB files, you’ll need to first prepare both independently using the Prepare tools in SAMSON:
- Remove solvent molecules, ions, or ligands that are not part of your study
- Remove alternate locations
- Add missing hydrogens
If the structures contain unresolved residues or atoms, you can repair them using the PDBFixer extension, which fixes sidechains, missing atoms, and incomplete residues.
Once cleaned, both structures must be merged into a single PDB file with the two conformations stored as different MODEL entries. Here’s the format:
|
1 2 3 4 5 6 7 |
MODEL 1 ... (start conformation) ENDMDL MODEL 2 ... (goal conformation) ENDMDL END |
This tells SAMSON to treat them as two conformations of one structure, which is necessary for the path search to work properly.
What if you don’t want to go through these steps today?
Good news: The Protein Path Finder tutorial file already contains a pre-prepared model of Adenylate Kinase, with two conformations labeled 4AKE (open) and 1AKE (closed). You can instantly load the model in SAMSON by downloading the document from this link:
https://www.samson-connect.net/documents/5eb7990e-fa44-4595-ab2c-99b6c68eada9
This saves time and lets you jump into running your first protein transition search!
Tips for working with your own systems
Be sure to keep these in mind when preparing your own protein structures:
- Check for missing heavy atoms or side chains before merging files
- Use consistent chain names and ordering in both conformations
- Double-check atom naming conventions
- Make use of Protein Preparation and Validation workflows in SAMSON
Once everything is set up correctly, you’ll save time and avoid frustration when launching your transition path simulation.
To learn more about how to use the full Protein Path Finder pipeline, visit the official tutorial page.
SAMSON and all SAMSON Extensions are free for non-commercial use. Download SAMSON at https://www.samson-connect.net.