the criteria that need to be used as template sequence for homology modeling

Question

[Sarah Diana]

Hi,

In term of Homology Modelling technique, what criteria that should have in template sequence to be chosen as the template structure in order to choose as the best template for the target sequence? E-value, identity, Gaps, query etc?

Answer 1

[Thind amarinder]

For homology modeling Identity, coverage and E-value all are significant. First choose the template with highest coverage and then look for identity if identity is more than 40 % , Then proceed further (But remember, structure ll be predicted only for coverage sequence).

Why to choose highest coverage, Because blast tools, calculate the Identity based on coverage. E.g. if result showing 50% identity and 50% coverage that means your template sequence covers the 50% sequence of target and out of that 50% sequence half sequence is identical. So overall identity is 25% in this case.(No doubt it will build the half structure of the protein). No structure will be predicted whatever sequences is not covered in the coverage.