I have the sequence of the protein that I want to model and I have two proteins with 3D structures that can be downloaded from PDB.org. The two likely template proteins being considered were obtained from BLAST on NCBI. One has 46% sequence homology but is a mutant protein. the other has 27% sequence homology but not a mutant protein. I would like to know if it is ok to use the mutant protein with 46% seq homology as template for constructing the homology model for my target protein.
46 % identity is also seems to be low, and for 27 % identity, no question to be used as the model. It is definitely something else. 46 % identity is not good enough either. This kind of sequence homology appears for the cross kingdom protein sequences. Define your study model and then proceed accordingly.
But I don't understand what kind of modelling you wanted to perform with only one sequence?
Olatomide Fadare Yes go ahead with using 46% structure as your template for homology modelling. If you are unlucky getting too many loops, they you might need to perform threading technique to model your protein.
Hi Olatomide Fadare ,
Selection of template is a really tricky stuff to deal with , in general, homology >50% is assumed to be suitable as a template. I will suggest you to try multiple template modelling , try Easymodeller tool. If you really find the task too hectic you can model your protein using ITASSER server.
Hope, it helps.
Best Wishes
Pankaj
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