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 -- modeller-care@salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage