ADL: free pdb file creation

Tomek Wlodarski tomek.wlodarski at gmail.com
Thu Mar 6 01:58:11 PST 2008


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

On Thu, Mar 6, 2008 at 12:17 AM, Larry Layne <llayne at andrew.cmu.edu> wrote:

> Hairat,
>
> I've found that The Dundee PRODRG Server (
> http://davapc1.bioch.dundee.ac.uk/programs/prodrg/) has a nice program
> that allows you to create PDB files among other popular types.  By clicking
> on the "draw molecule with JME" link, it will input the structure into the
> text box further down the screen and then give you the choice in the type of
> file format you want it in.  I found it to be very good when I need a
> program to  preserve conjugated aromatic carbons.  All they ask for in
> return is to cite them in any publications.
>
> Happy Docking!
> Larry
>
> > ----------------------------------------------------------------------
> >
> > Message: 1 Date: Wed, 5 Mar 2008 03:26:23 +0000 From: Hairat Sabit
> > <hairat at hotmail.com> Subject: ADL: pdb files To: <autodock at scripps.edu>
> > Message-ID: <BAY140-W3932DA4E36AFC69350CC1C8110 at phx.gbl> Content-Type:
> > text/plain; charset="iso-8859-1"
> >
> >
> > Dear all, What are the good softwares (free) to generate small molecules
> > .pdb or .mol2 files for Autodock?I appreciate your inputs.Hairat
> > _________________________________________________________________ Shed
> > those extra pounds with MSN and The Biggest Loser!
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> > ------------------------------
> >
>
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