[Dock-fans] Fixing protonation state

[Scott Brozell]

Hi,

On Fri, 26 Oct 2007 burgosgu at ualberta.ca wrote:

> I need to have a compound correctly protonated to dock it. I tried to  
> use the resource of
> "upload sets" of ZINC, but it seems that it does not have the required  
> charactersitics of
> bioavailability and non-toxicity, because it gives me no output as it  
> did with other
> compounds.
> 
> The smile for this compound is:
> C1=C(C=CC2=C1C(=C[N]2)CC(=O)NCCCNCCCCNCCCNC(=O)CC3=C[N]C4=C3C=C(C=C4)Br)Br

There are a number of options:

smi23d - 3D Coordinate Generation
http://www.chembiogrid.org/cheminfo/smi23d/

Online SMILES Translator and Structure File Generator
http://cactus.nci.nih.gov/services/translate/

Molecule file conversion with MolConverter
http://www.chemaxon.com/marvin/doc/user/molconvert.html

Search the CCL for others:
http://www.ccl.net/


Once you get an xyz representation then you can apply other tools
to study and modify the protonation, such as Chimera, reduce, LEaP, etc.

Scott