I would like to know about the result display of the autodock function.
While PDB shows the interactions between Ligand and Protein, these interactions are not displayed in datagrok’s results. (More precisely, interactions within the protein are shown in PDB.)
Since Ligand/Protein interactions are important factors in interpreting docking results, I would be grateful if you could investigate this if possible.
Thank you for pointing this out! We completely understand the importance of showing ligand/protein interactions in docking results. I’ll look into how we can improve the visualization in Datagrok to include these interactions and will get back to you soon with the results.
Dear Oleksandra,
Thank you for your positive feedback and I appreciate datagrok team has already issued ticket for that. If you have any questions or comments, please let me know.
Just for your information, autodock result in Datagrok included three structures as shown below. On the other hand, structure from PDB has one single structure. That can be a reason for not showing interaction. I hope it might be helpful for you.
Thank you for providing the additional details!
I believe you’re absolutely right — this could very well be the reason why the interactions aren’t showing up.
