a plant compound was used against virus to stop the attachment of virus on the cell (in-vitro) and experimentally proved also that but the exact mechanism was not found for this. I did a blind docking in AutoDock Vina to find the putative binding site for that ligand on the protein. One particular ligand pose was found on a very important pocket of the viral protein but it ranks at the 7th position in the result given but Vina. Can I still use that pose for furthur study?
Yes, you could use the pose for further study. Blind docking, where the entire protein is placed inside the simulation cell, can produce a number of poses with favorable free energies of binding. Selection of poses for further study can be guided by additional data that you might have about the protein. You could refine the pose of interest by doing further docking studies, placing that particular site at the center of a smaller simulation cell.
Thank you so much Dr Rudy.
It would be of a great help if you can provide a reference for this.
- Badges
- Science topic
- Similar topics
- Biological Science
- Microbiology
- Virology
- Virus