I have a protein seq with 1200 amino acids and when i searched for its templates, I am getting its match till 979 amino acid.
When I constructed its model by modeller I got models with 1053 amino acids.
How to model the remaining protein as the reaming part contains important domains.
Try using iTasser it will give you the most likely predicted structures.
http://zhanglab.ccmb.med.umich.edu/I-TASSER/
Most protein modeling programs use homologous structures, so keep in mind that when there are no homologous structures known for the C-terminal part, modeling may be unreliable.
If you know that your c-terminal region contains important domains, you should be able to model that region as well. Conversely, if your c-terminal region is disordered (you can check using the disorder prediction server d2p2) as Tjaard pointed out, the model will not be reliable.
https://d2p2.pro
I think I-tasser would be better option . If u know about the rest part of your protein if its loop part u can model loop part also using Schrondinger Prime suite.
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