ADL: Energy Minimization

Tomek Wlodarski tomek.wlodarski at gmail.com
Thu Mar 6 11:59:43 PST 2008


 Dear Mihaly Mezei,

I agree with you that "binding free energy estimate includes the energy of
the ligand in the initial conformation".
But in publication which I have cited above from J. Comp. Chem is claimed
that on protein test set AD4 gives better results, when ligand initial
conformation was extended conformation, and the worst results gives compact
conformation.
"Based on these results, we have chosen the extended conformation as the
default unbound state in AutoDock4"
So for my studies I used not EM ligand structure- only extended.
Best,

Tomek Wlodarski


On Thu, Mar 6, 2008 at 8:20 PM, L. Michel Espinoza-Fonseca <
mef at ddt.biochem.umn.edu> wrote:

> Yes. For small molecules you can use VEGA:
>
> http://www.ddl.unimi.it/vega/index.htm
>
> This is a free program that can perform energy minimization at
> semiempirical level. Pretty good and easy to use.
>
> For proteins, the easiest program to use is the Swiss PDB viewer:
>
> www.expasy.ch/spdbv/
>
> Then you also have NAMD and GROMACS, which are more robust when it
> comes to energy minimization.
>
> Cheers,
> Michel
>
> On Thu, Mar 6, 2008 at 1:07 PM, George Tzotzos <gtzotzos at mac.com> wrote:
> > 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<http://inka.mssm.edu/%7Emezei>
> >  > ________________________________________________
> >  > --- ADL: AutoDock List  --- http://autodock.scripps.edu/
> >  > mailing_list ---
> >
> >  ________________________________________________
> >  --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list---
> >
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>


More information about the autodock mailing list