Hi,
I have predicted the structure of a membrane protein using I-TASSER.
The link is below.
http://zhanglab.ccmb.med.umich.edu/I-TASSER/output/S239441/
Regarding N-terminal and the C-terminal, I feel that they are not modeled properly by I-TASSER. As the N-terminal and the C-terminal are intracellular, I expect that these two ends should face towards cytoplasm; however, this is not the case with my protein.
Do you think that I should refine the N-terminal and C-terminal ends using Chimera interface to Modeller using Loop refine tool. After that I can choose the best model, which I can submit to ModRefiner for overall energy minimization.
Do you think I am correct in my approach. Your suggestion in this regard would be really important as I am new in this field.
Sincerely,
Tikam Chand