I want to make high throughput screening by MOE and when i made the validation, RMSD value was very high. I changed the following parameters: Placement, rescoring1, refinement and rescoring2 and tried all its options but none of these changes gave rmsd lower than 2. Should i change the ligand - enzyme complex or change the program?
First of all, you should re-check the docking protocol. Follow the actual guideline of MOE docking. Then you may change the ligand-enzyme complex.
Hello, which version of MOE are you using? Also, which forcefield are you applying to protein preparation and docking? If you are using GBVI/WSA scoring maybe that is the issue. Re-check your preparation and change forcefield if necessary, in my experience Amber12:EHT works good with docking.
I think it is a good idea to try a different docking program. If this is not working, you might try to dock with constraints. For example, maybe there are important protein-ligand interactions know from the literature, which you can define as pharmacophoric features and use as pharmacophore constraints in MOE and then apply the same constraints for high throughput screening. If you can not re-dock the co-crystal ligand, it indicates, that the protocol is not working very well. Therefore, changing complex for validation will only mask the problem, but will not solve it. Good luck!
Thank you all very much
Fernando Prieto-Martínez the forcefield im using is MMFF94x and i tried to use GBVI/WSA for scoring but the RMSD was high too
i will try to change the forcefield as you said
- Badges
- Science topic
- Similar topics
- Correction