I have a question of modelling the C-terminal region of my target. The protein matches with the crystal structure templates except the C-terminal region (named as C-tail here). I did BLAST search using this segment to against the proteins with known structures at Protein Data Band. It returns a match with a short region of an antibody at 56% sequence identity with the inclusion of 4 gaps. The function of my target protein has nothing to do with antibody. I am not sure if it is reasonable to use the BLAST match results as templates to model the conformation of the C-tail.

I have thought to model this C-tail region using the “Loop Model” in Modeller. There are some concerns here. First, the C-tail contains 24 amino acids. Will this be too long for the loop-model in Modeller? If the length is not the problem, how reliable are the conformations of the segment? Second, the segment is at the C-terminal of the protein. For my understanding, the “Loop Model” in Modeller requires the N’ and C’ terminus of the segment to be fixed. The position of the last residues of the segment will have significant influence on the “Loop” conformation. Which one is more reasonable, to model this segment based on the sequence homology, or use a loop modelling algorithm?