VINA OUTPUT ANALYSIS
Vina output analysis using Discovery Studio visualizer
Image Credit: Stock photos
“In previous articles ("Tutorial: Vina Output Analysis Using PyMol" and "Video Tutorial: Autodock Vina Result Analysis with PyMol"), the analysis of Autodock Vina [2] result using the Pymol viewer [3] was explained.”
he discovery studio (DS) visualizer [1] offers several features for analyzing docking results. In previous articles ("Tutorial: Vina Output Analysis Using PyMol" and "Video Tutorial: Autodock Vina Result Analysis with PyMol"), the analysis of Autodock Vina [2] result using the Pymol viewer [3] was explained. In this article, the Autodock Vina result is being analyzed in the DS visualizer [1].
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To visualize Autodock Vina results in DS visualizer, you need the same files as used for the Pymol viewer: protein in .pdb format (here, 2bxa.pdb) and vina output file (here, SO.pdbqt). 1. Open DS visualizer.
2. Open “2bxa.pdb” and “SO.pdbqt” files.
3. In the “pdbqt” tab, you will see a dropdown in a new left panel showing different poses of the ligand named as model_0, model_1, and so on. Click on one of these poses and the ligand will switch its position on the screen. Select one of these poses, say, “model_4”, --> rightclick on the blank space --> click “Copy”.
4. Go to the receptor tab, here, “pdb” --> rightclick on the blank space --> click “Paste”. After
that, you will see the ligand somewhere within the protein. But it is not showing any interactions yet.
5. To see the interactions between the protein and the ligand, look at the panel in the left corner for “Display receptor-ligand interactions.” Just below this, click on “Ligand interactions”. After that,
you will be able to see the interactions.
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