I am currently working with MOE to dock a database of compounds. My main issue comes up when retrying the docking process. I get different results for the same compounds suing the same procedures.
If you are not getting the same (or identical) results, I think you are not sampling the docking binding site well enough.
Increase the number of generated poses (don't use the default 30, try 250) and/or change the scoring method.
Hope it helps!
I have a long experience with MOE program which I feels is a good program suite. The issue must be with the procedure. If you are using pregenerated ligand database for both the docking procedures, then it must be with the protein binding site info and docking procedure only. The difference might comes from selecting the active site residue or dimensions (angstrom) or flexibility. check thoroughly.
However, I also wanted to know your scale of comparison between the dockings. You should be checking atleast top5 poses energies and their localization. Little variation in ranking may be possible. Sometime due to very less variation between the docking scores, algorithm may not be able to differentiate ranking; but that totally based on the exhaustiveness which is inbuild in the docking types. For that reason, if you sole aim is comparison then my suggestion is to use highly refined grid and most accurate docking method of a particular program.
Different docking results using the same procedure imply an element of randomness, not unusual in docking algorithms; i would generate many docking poses (500) to reproduce the docking results.
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