Hi, you should probably try to re-score your solutions. That's what we typically do with an in-house developed re-scoring function.
Depends on the purpose of the docking study: if it is to explain the SAR, analyze the low-energy poses to see which pose can explain the SAR trend. If the purpose is screening, then check how much the low-energy poses vary in their orientation in the binding pocket. Either way, its always a good idea to validate your docking software and/or methods by re-docking the native ligand, if any, of a crystal structure. It would also make sense to repeat the docking using a different software or rescore the poses using a different scoring function as mentioned in the post above.
Hi Khatereh,
Agreed with Mr Sudhir and Mr Sergei.
The best trend to validate the docking results are:
1.select good poses (RMSD difference with known crystalized struc)-----> MD (to optimize the complex)-----------> MM-(GBSA/PBSA)
2.select good poses (RMSD difference with known crystalized struc)-----> amberscore(dock6.6, rescoring purpose)
Hope this helps
Searching for key interactions between the docked ligand and the receptor site is often good
computing the RMSD between the experimental ligand (if it exists) and the docked pose is another good approach
It may also be interesting to verify of the fingerprint study and the protein-ligand interactions could explain the SAR
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