Re: [modeller_usage] question about modelling a small oligiopeptid.

[Knut J Bjuland <>]

On 02/09/2010 08:07 PM, Modeller Caretaker wrote:
> On 02/09/2010 06:00 AM, Knut J Bjuland wrote:
> > Can modeller do modelling of a small oligio peptid. The peptid should be
> > 4 amino acid long and i should start with Met-Glu and 3 and four could
> > be any peptid. If modeller is not up to the task what software is best
> > suite to desing ligand that are 4 amino acid resideus long.
>
> Modeller is a tool for homology or comparative modeling. Assuming you 
> have some kind of score to distinguish "good" peptides from bad ones, 
> what you are describing sounds like protein design to me. This is not 
> something that Modeller does, but you might want to take a look at 
> Rosetta, which I believe includes a design module.
>
>     Ben Webb, Modeller Caretaker
I have already use Modeller to build a protein, but what I was thinking 
about was ligand design. I would also take a look at Rosettea. Ligand 
desgin is the pice I am missing before I start using the model from 
Modeller in combination with dock 6.1.

Knut J