I did molecular docking using autodock-vina and found great score of binding affinity. But when I dive on to see the protein-ligand interaction I did't found any h-bond among many of my bond interactions.
Question :
1. How much h-bond affect on protein-ligand interaction?
2. Should I overlook what I get and continue my job?
AutoDock Vina requires polar hydrogens to determine hydrogen bonds. Did you add polar hydrogen to your coordinates before conducting the docking?
Yun-Tzai Lee Thank You for your response.
I did it. But every time I got the same result. Today I do my protein and ligand preparation with chimera software and get the same result. However, my protein has 4 chain and I docked my ligand with each of chain individually and one of the chain showed hydrogen bond interaction and rest of chain do not show h-bond interaction. Now, I am confused what to do.
Don't be discouraged, it is getting interesting. Try to align the structures of each chain. Perhaps, there are subtle structural differences in the ligand docking region. Sub-angstrom difference as to hydrogen bond has immense effect. It may fail for docking software to define the hydrogen bond.
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