Manually configuring a protein docking setup can be tedious and error-prone, especially when dealing with complex biomolecular structures. One common difficulty for molecular modelers is quickly and accurately preparing a system for docking simulations while minimizing preprocessing time.
Fortunately, SAMSON and the Hex Extension streamline much of this process. In this blog post, we’ll look at how SAMSON simplifies preparing and setting up docking simulations between two proteins, getting you dock-ready in minutes instead of hours.
Step 1: Load the Example System (or Your Own)
Start in SAMSON by downloading the sample document from:
https://www.samson-connect.net/documents/575f78c0-27b9-4f24-bc39-78cf1d52ecc2
This document contains two proteins: 2PTC_E and 2PTC_I. These represent the receptor and ligand for your docking simulation.
Step 2: Prepare the System
With the sample loaded, head to Home > Prepare. Tick the boxes to:
- Remove atoms with alternate locations
- Remove water, monatomic ions, and ligands
- Add hydrogens (unless your system already has them with specific protonation)
This one-click approach cleans the structure and ensures it’s ready for docking.
If your structure has missing residues or atoms, consider using the PDBFixer extension to automatically repair it.
Step 3: Load the Hex App
Activate the Hex app via Home > Apps > Biology > Hex (or search for it with the search bar). You’ll now access a UI to define docking parameters and identify the two docking partners.
Set 2PTC_E as the receptor, and 2PTC_I as the ligand.
Want to re-run different docking trials using the same starting pose? Save the initial ligand conformation via Edit > Conformation.
Step 4: Define Docking Range
Restricting the docking search domain can save computation time and improve prediction quality. Click on Advanced parameters and set both receptor and ligand range angles to 45 degrees.
This constrains the rotational space explored, creating a focused docking search around biologically meaningful orientations.
Why This Matters
By using SAMSON’s interface and the Hex Extension, molecular modelers don’t have to go through dozens of preprocessing steps manually. Everything from hydrogen addition to visual alignment happens through a streamlined graphical workflow.
This is especially helpful in educational or rapid prototyping contexts, where time and reproducibility matter. You can also modify advanced parameters, animate docking results, and perform in-depth analyses—all in the same interface.
To learn more about setting up and running docking simulations, check the full documentation at this link.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.