Analyzing protein–ligand interactions is a key step in molecular modeling and drug design. Whether you’re a student, researcher, or experienced computational chemist, you’ve probably found yourself trying to figure out a fast and visual way to confirm whether your ligand binds as expected — or better, how it interacts at the atomic level with its target.
Instead of spending time writing custom code or switching between multiple tools, SAMSON offers a visual and efficient approach to interaction analysis using its freely available, integrated Protein-Ligand Interaction Analyzer.
Why is this useful?
After a docking calculation — for example using the FITTED Suite — it’s often necessary to validate how well the ligand fits and interacts with its receptor. Does it form hydrogen bonds? Does it target key residues in the active site? You shouldn’t have to export files, launch external tools, or decipher tables to get those answers.
SAMSON includes several tools that make structure-based interaction analysis accessible and even a bit enjoyable 😊. Let’s take a tour through one example workflow using a protein–ligand complex loaded in SAMSON.
Step-by-step: Visualize Key Interactions
1. Load Your Receptor–Ligand Complex
This could be a crystal structure or the output of a docking calculation. For this example, say you’ve just completed a FITTED docking with the thymidine kinase protein (1E2K) and the ligand TMC 500.
2. Launch the Protein-Ligand Interaction Analyzer
From the top-level menu bar, go to Home > Apps > Biology and select Protein-Ligand Interaction Analyzer, or find it quickly via the search bar by typing part of the name.
3. Set Receptor and Ligand
Click on your processed receptor (e.g., 1E2K_pro) and hit Set under the Receptor field. Then choose your ligand pose (e.g., 1E2K_log.mol2_DockingRun_*) and hit Set for Ligand.
4. Click “Analyze”
SAMSON will now compute contact areas, detect potential hydrogen bonds (H-bonds), identify surrounding residues, and present relevant metrics — all in just a few seconds and within the same workspace.
5. Bonus: Visualize H-Bonds with One Click
Want a dedicated hydrogen bond visual? Open the Hydrogen Bond Finder Extension. You can select both the ligand and receptor, choose the H-bond detection mode, and instantly get a visual overlay of hydrogen bonds in the 3D view.
That’s it
The ability to go from docking results to labeled interaction visuals — with ribbons, binding site residues, and even color-coded atom types — without leaving your modeling environment is a big time saver. You can even export result tables or build high-quality visuals for publication.
If you want to explore more detailed analysis tools, check the standalone Hydrogen Bond Finder, and dig into residue-level selectors and materials from the Visualization menu for enhanced 3D rendering.
Learn more in the full documentation here: FITTED Suite Tutorial.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net and get started right away.