simran jeet wrote: > I have a protein sequence whose N terminus region does not matches with > the template. Is it neccessary that N and C terminus regions of a > protein should be fixed for homology modeling? The n terminus region > contains 12 residues. There are long gaps also within the > alignment. Can these regions be modelled by loop modelling? I am also > attaching the alignment file.
You can certainly try to build a model without a template for the N or C termini, but what you'll probably find is that you'll just get very flexible regions with no secondary structure, so you're probably better off removing those regions from your target sequence. Gaps within your sequence up to about 8-12 residues should be amenable to loop modeling, providing you build enough models to get reasonable sampling.
Ben Webb, Modeller Caretaker