ADL: Energy Minimization

George Tzotzos gtzotzos at
Thu Mar 6 11:07:18 PST 2008

The Dundee PRODRG2 Server has the functionality of energy  
minimisation ( 

Does anyone happen to know of any other programmes accepting PDB  
structures for energy minimisation?



On Mar 6, 2008, at 6:11 PM, Mihaly Mezei wrote:

>> 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
> Voice:  (212) 659-5475   Fax: (212) 849-2456
> WWW (MSSM home): 
> WWW (Lab home - software, publications):
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