ADL: Energy Minimization

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


The Dundee PRODRG2 Server has the functionality of energy  
minimisation (http://davapc1.bioch.dundee.ac.uk/programs/prodrg/ 
prodrg.html)

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

Thanks

George


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): http://www.mountsinai.org/Find%20A%20Faculty/ 
> profile.do?id=0000072500001497192632
> WWW (Lab home - software, publications): http://inka.mssm.edu/~mezei
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