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.
Knut J _________________________________________________________________ Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. https://signup.live.com/signup.aspx?id=60969
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
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
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Knut J Bjuland -
Modeller Caretaker