Dear Research gate Users,
I have so far used AutoDock4, AutoDock Vina, GEMDOCK, DOCK and GOLD docking and VS suits. But each an everyone of the software would predict significant change in binding affinities for a single ligand docked in to a single protein. As I am aware all the software generates binding affinities in kcal/mol unit.
So how can these significant changes occur?
I have attached few comparisons of my results
You should be aware that, each software has its own prediction algorithm. So it is not the right way to compare the docking with different tools. Rather I would suggest you go with multiple times docking with the same software and compare the average binding score/energy/affinity. That will give you more appropriate results.
For better software consideration, you can go through the papers attached
Thirumal Kumar even if the prediction algorithm is different isn't it supposed generate a binding affinity specific to positioning of the ligand relative to the receptor. So even if the software algorithm changes all will finally calculate the binding affinity/energy. Comparing the docking algorithms of the above there isn't much change in the force field terms.
I wasn't comparing between algorithms. But It is difficult to validate my results without understanding how this can happen.
@Dinuka: That is the reason, I asked you to go through that two papers, those papers have already compared the efficiency of algorithms of different software. So you can choose one which is more appropriate to you. The docking can not tell you more information about the exact interaction. For eg. The positive value in binding energy also might pave interactions, those could be analyzed only with the higher level molecular dynamics. So validating blindly with the docking could have least impact in the scientific scenario.
- Badges
- Science topic