ADL: Energy Minimization

Larry Layne llayne at andrew.cmu.edu
Thu Mar 6 08:59:06 PST 2008


Tomek,

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.  

Larry

> Hi! PRODRG is a very nice way of doing this but I think it has some 
> disadvantages: - without energy minimization structures are very unreal -
> with EM are not the best option for AD because in ref: Huey, R., Morris, 
> G. M., Olson, A. J. and Goodsell, D. S. (2007), A Semiempirical Free
> Energy Force Field with Charge-Based 
> Desolvation<http://www3.interscience.wiley.com/cgi-bin/abstract/114107459
> /ABSTRACT> *J. Computational Chemistry*, *28*: 1145-1152 Authors claim that
> extended form of ligand is better option for docking than compacted(after
> EM) I suggest also very easy to use CORINA: 
> http://www.molecular-networks.com/online_demos/corina_demo.html It
> generates ligand structures in extended form. I hope this would be helpful
> for you Best,
> 
> Tomek Wlodarski
> 





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