Hi,
I have a bit of doubt in homology modeling. Is it advisable to align one template to a specific region, say from amino acid 80 - 150, or using a few templates for that specific region?
Thanking you in advance!
-Elmo
If there is a template available with fairly high sequence similarity you should probably just use the one template. Otherwise it may be advisable to use a few different ones and compare the results. I've typically tried a few different templates and qualitatively compared the final output models just to make sure there were no major differences, especially around known catalytic or active sites, binding sites, or other important domains. Most of the time you probably aren;t going to see huge differences, and it also really depends what you are using the homology model for in terms of how accurate you think it needs to be.
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
version 2.3.6
A good paper on this issue is: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2386743/
It concludes with similar points. Noteworthy is that using multiple templates may be useful when the different templates have higher sequence identity and are thus better for specific regions. This may not be as relevant for as short a sequence as the OP mentions.