I am new to Homology Modeling and I really feel that what I did was not really right. Please, I need some advice / comment. I have a protein sequence of 500aa in length and did a BLAST on my protein sequence. Only the 150 - 470aa belongs to a common domain but the residues from 1 - 149 and 471 - 500 doesn't show any common domain. Thus, I break them into fragments (1 - 149, 150 - 470, 471 - 500) and I used HHpred to search for templates and modeled them out individually. Is it right? Now I'm not very sure how can I join them together.
Previously, what I did was inputing the whole protein sequence (1 - 500aa) and letting HHpred to do loop modeling for the regions from 1 - 149 and 471 - 500. Then when I check it with Verify3D and other verification programs, they "complain" for those region being loop-modeled. I am not sure if i can proceed with this model for further investigation like docking and so on. However, the region that was covered (150 - 470) was the part I am targetting for docking later. Can I still proceed? Or align them by fragments like mention earlier? If yes for the later, please can someone please tell how to join them back together.
Thanking you in advance.
Best regards, Elmo