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