I tried protein-ligand (small molecule) docking using AutoDock Vina. Before docking my compound of interest, I tried to validate the docking procedure using a known crystal structure from the PDB. I prepared both protein and the ligand and run the docking. Though I was able to maintain the same binding site, the ligand was inverted 180 degrees. This just happened for the standard ligand, my own new compounds, and for other ligands. Though I am happy I maintained similar binding sites, I am wondering why all ligands are inverted.
What is wrong with the ligand preparation or the overall procedure.
Thanks in advance for your help.
Dessalegn Gelayee Hi
After preparing ligand(interested), find out the coordinate of ligand which present in protein already then generate the grid and after deleting ligand of protein then as usual protocol follow.
I recall seeing this problem on the Autodock FAQ site some 10 years ago. It apparently was a bug. Perhaps it was not repaired or it has somehow recurred. I suggest checking the Autodock forum.
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