To validate one of our research methods, we used the PDB ID: 5MRK (Structural basis of Zika virus methyltransferase inhibition by sinefungin) as our standard. When we do the docking simulation of Sinefungin, we obtained the RMSD of each docking pose about 0.8362 Å and 0.8132 Å from rigid docking and flexible docking approach, respectively. Is this tolerable, or should we use any other parameters that resulted lowered RMSD value than this one?
Hi, Mochammad Arfin Fardiansyah Nasution,
While performing docking, we aimed at obtaining a binding conformation of the selected inhibitors. Therefore, we go for the validation of the docking algorithm. For that, we validate our protocol by calculating RMSD (redocking) value of the experimentally determined protein-ligand complex (like in your case: 5MRK). While redocking, you must obtain a pose which is similar to the experimentally determined one, which means your docking protocol is validated. Now, if you are getting RMSD value less than 1.5 Angstrom, then it is good to consider.
The value less than 1.5 Angstrom is tolerable in the docking protocol.
Less than 1.5 A is acceptable, less than 1.0 is very good. It used to be the case that 2A was the generally recognised acceptability cut-off, but as docking programs have improved, this is no longer so.
It is worth pointing out that very low RMSDs (
in view of the fact that getting RMSD value of zero is impossible, we therefore give some sort of flexibility in the validation procedure. Thereby,
The acceptable RMSD depends on the size and the number of torsion angles of the ligand. It is not the same to dock a large flexible ligand than a small rigid one. Our experience indicates while 1 to 1.5 A is OK for the latter case, you can use 2.0 A RMSD for the former.
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