On 02/05/2014 02:03 AM, Juan Munoz-Garcia wrote:
I want to do homology modelling of a protein based on just one template because it is so far the only template of a particular protein state of its family I' m interest in. However, that template does not contain the natural ligand of the target. Then, I want to use another template of the protein-ligand(natural) complex of interest but just to say Modeller to use the ligand coordinates. So, it is a multi-alignment using the HET option but I don't know how to say Modeller that I just want to model the target sequence based on just one template and considering the ligand of the other template. Is this possible?
This is simply done by modifying the alignment to align the first template with the model in the "protein" region, and the second template with the model in the "ligand" region. Note, however, that you can't use *just* the ligand from one template - you'll have no constraints on it and so it will likely wander away from the protein during the optimization. You should try to incorporate at least some of the nearby protein from the second protein, so that Modeller can deduce protein-ligand restraints.
Ben Webb, Modeller Caretaker
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