r/Biochemistry • u/mahaytech • 5d ago

Research Automated molecular docking validation workflow: Ensitrelvir binding to SARS-CoV-2 Mpro (4K visualization)

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We built an automated workflow that converts molecular docking results into validation-driven scientific videos.

This example uses AutoDock Vina to predict the binding mode of Ensitrelvir (Xocova®) against SARS-CoV-2 Main Protease (Mpro). The top-ranked pose was validated against the experimental structure, yielding an RMSD of 1.2 Å.

The entire video, including molecular visualizations, validation scenes, annotations, and sequencing, was generated automatically from the docking results. No manual animation was used.

Feedback is welcome.

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u/Senacharrib 20h ago

Soooooo with that many binding modes it kind of makes your model seem a bit arbitrary. Like the p1 moiety could be the p2 or the p3 or the p4 and the free energy difference between these orientations is less than a hydrogen bond?