After doing protein-protein docking using ZDock, is it necessary to perform the RDock protocol? How can it affect my results?
The purpose of RDock and ZDock are different.
ZDock is suitable to protein-protein docking. Whereas RDock is mainly for protein-small molecule docking. You should decide based on the two molecules you want to dock. If you want to dock another protein or large peptide against a protein, then go for ZDOCK. If you want to dock small molecule or small peptide against a protein, then go for RDock.
It is not necessary to perform one protocol if you are performing other protocol. Two are independent algorithms.
actually I am asking for RDOCK, which is a refinement program used for better scoring after ZDOCK
Dear Ria,
ZDOCK uses a fast FT (Fourier transform) to search all possible binding modes for proteins, evaluating based on shape complementarity, electrostatics and desolvation energy. The top 2000 predictions from ZDOCK are then given to RDOCK where they are minimized by CHARMM to improve the energies and eliminate clashes. Then the electrostatic and desolvation energies are recomputed by RDOCK (in a more detailed fashion than the calculations performed by ZDOCK), that signifies its importance.
Best wishes,
No its no important but when you want to analyz the interaction residues of both of the proteins then you have to go to RDock.
to understand interface region, and interacting residues between protein-protein or protein-peptide interaction, consider R dock.
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