For molecular modelers, understanding and presenting protein-ligand interactions at a binding site is a core challenge. Whether you’re analyzing self-docking workflows or reviewing structural models, visualizing the binding site and surrounding residues can clarify essential molecular insights. This post walks you through a practical workflow for visualizing ligand binding sites in SAMSON using the FITTED Suite SAMSON Extension. No matter the complexity of your model, this tutorial will guide you to make your ligand-receptor visualizations more interpretable and impactful.
Step 1: Setting Up Your System
After completing your docking workflow with FITTED, your SAMSON document will show the processed receptor (e.g., 1E2K_pro) and the resulting ligand pose. To begin visualizing the binding site, first hide the initial receptor structure by unchecking it in the Document view. This prevents overlap with the newly processed data.
Next, add a Ribbons structure visual model to visualize the protein’s secondary structure. Do this by selecting the processed receptor in the Document view and then using the Visualization menu. Afterward, hide the receptor’s structural model while retaining the added visual model.
Step 2: Highlighting Residues Around the Ligand
To visualize residues that interact with the binding site, start by selecting the resulting ligand (e.g., 1E2K_log.mol2_DockingRun_*).
Then, navigate to Select > Biology > Binding sites and set radius parameters to include residues near the ligand. This selection allows you to focus exclusively on the binding site:
You can save this selection in a group for organization (e.g., “Binding site residues”). To create the group, click on the Current selection button in the Document view and choose Create group.
Step 3: Adding Visual Models
With the residues selected, add a Licorice visual model to them via the Visualization menu. This highlights atomic connections within the receptor-ligand interface. Select carbons in the receptor residues by navigating to Select > Atoms > Carbons, then apply a color scheme based on residue sequence number for clearer interpretation.
To layer this visual clarity, choose Material > Per attribute from the Visualization menu and select Residue index. Hide the receptor’s structural model for a streamlined display, emphasizing the interactions.
The final visualization may look like this:
Adjust elements further using the Inspector, which allows you to modify the styles for labels, carbons, or residue appearances as needed.
Why It Matters
Clear visualization of ligand binding sites enhances communication of molecular design concepts. Whether for presentations, publications, or personal understanding, SAMSON’s tools for rendering secondary structures and atomic details ensure higher interpretability of docking results. Being able to customize displays and focus on chemically relevant regions is what makes SAMSON especially useful for molecular modeling and design workflows.
To learn more about the FITTED Suite and how it can streamline your workflows for both covalent and non-covalent docking, please visit the official documentation page.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON for free at SAMSON Connect.