One Or Many Templates For Aligning To One Specific Region For Homology Modeling?
2
0
Entering edit mode
10.8 years ago
Elmo ▴ 130

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

homology-modeling • 2.4k views
ADD COMMENT
2
Entering edit mode
10.2 years ago
DG 7.3k

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.

ADD COMMENT
1
Entering edit mode

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.

ADD REPLY
0
Entering edit mode
10.2 years ago
Pappu ★ 2.1k

Use I-Tasser server.

ADD COMMENT

Login before adding your answer.

Traffic: 1385 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6