Hi, I am building a protein model based on templates and secondary structure restraints. My protein is 781 amino acids long, and it has two homology derived templates in the 1-92 and 394-412 segments. The 590-781 segment has a solved crystallographic structure. I have given the corresponding templates to these three segments. I have also added secondary structure restraints to the remaining parts of the protein based on secondary structure predictions. The problem is that when I plot the DOPE profiles of the generated models, I see that the template-based segments (especially the 590-781 segment) have the highest energy. This makes it impossible to refine only the parts of the model with high energy, since the refinement will destroy the structures that must be present in the protein. I have used the standard scripts for model making and restraint-adding incorporated in Modeller examples.
I would like to know the reasons for getting high energy in the part of the protein, which has a solved crystallographic structure. I will appreciate any advice. Thank you.
On 05/02/2011 03:57 AM, Lilit Nersisyan wrote: > The problem is that when I plot the DOPE profiles > of the generated models, I see that the template-based segments > (especially the 590-781 segment) have the highest energy.
DOPE is an assessment method which aims to tell you how close to native a model structure is. Like any assessment method, it cannot always make this determination with 100% accuracy. Since you know these segments are native-like anyway, I would suggest you trust that information over what DOPE is suggesting.
Ben Webb, Modeller Caretaker
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Lilit Nersisyan -
Modeller Caretaker