Hi everyone
I optimized my ligands with gaussian. I want to dock these with Discovery Studio.
is it necessary to minimize or prepare or apply forcefield to my ligands before doing docking.if so, which one should be done?
Thanks in advance
Prepare the ligands and as well as the receptor. Minimize both the receptor and ligands. Define the cavity and do the docking.
Hi, your ligands and receptor should be optimized regarding geometry and energy before perform molecular docking.
Hi
Do watch the attached link
https://www.youtube.com/watch?v=Lgyoh9xzakg
Regards
Anu
Hello
Free version of Discovery Studio has not this ability to do docking, however, for docking of ligand-protein the first step is deep understanding of ligand and protein mechanism and recognize of protein active site based on their action to cause or make disease.
In practical step for docking after optimization of ligand that you do it by gaussian in the most case you don't need to optimize the active site of protein because this action will change the cavity shape of protein that will proceed by crystallization of protein in X-ray crystallography.
the best
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