Hi,
a protein i am dealing with has some missing residues. I am trying to build it with modeller. How could i verify the structure generated? Also the remarks says, CA 5% of the side chains are poorly defined and are currently modelled as alanines. Do any one know the meaning of this remark. Should i do any thing as part of correcting the structure for md simulation?
On 4/8/13 2:22 AM, Mary Varughese wrote: > a protein i am dealing with has some missing residues. I am trying to > build it with modeller. How could i verify the structure generated?
This is simply a comparative model, where the structure with the missing residues is your template. So you'd verify the structure in the same way as any other comparative model, e.g. using an assessment method such as normalized DOPE.
> Also the remarks says, CA 5% of the side chains are poorly defined and > are currently modelled as alanines.
If the correct sequence is available in the SEQRES records, you should probably use that in your model.
Ben Webb, Modeller Caretaker
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Mary Varughese -
Modeller Caretaker