ADL: Energy Minimization

Mihaly Mezei Mihaly.Mezei at mssm.edu
Thu Mar 6 09:11:12 PST 2008



> Is energy minimization necessary since autodock is just going to 
> twist the molecule around anyway?  It seems like an unnecessary 
> step to me, and it looks like that is what you just quoted in from 
> the J. Comp. Chem. article.  
Actually, it is important to energy minimize, since the binding free energy estimate includes the energy of the ligand in the initial conformation. I once found a ligand whose binding free energy was estimated as ca -50 kcal/mol, due to some clashes int he initial conformation.

Mihaly Mezei

Department of Structural and Chemical Biology, Mount Sinai School of Medicine, NYU
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