Modeling large protein sequence having homologues with less similarity.
Hello, My target sequence of protein is too large containing more than 1000 amino acids and I found 4 homologues in PDB showing very less similarity i-e. two showing 28% similarity, one showing 24% and last one showing 19% similarity with my target sequence. Also the starting residues of templates have no homology with my target sequence and Modeller has to read from 1st residue of template, that bocomes impossible in this case. So now how can I model my target sequence?
On 07/06/2009 12:27 AM, Sehrish Batool wrote: > My target sequence of protein is too large containing more than 1000 > amino acids and I found 4 homologues in PDB showing very less similarity > i-e. two showing 28% similarity, one showing 24% and last one showing > 19% similarity with my target sequence.
Depending on your alignment method and the fold assignment, that may be OK.
> Also the starting residues of > templates have no homology with my target sequence and Modeller has to > read from 1st residue of template, that bocomes impossible in this case.
I don't know where you got that idea from - Modeller does not have to read from the first residue of each template. You can read any contiguous range (if the range is not contiguous you can simply edit the PDB file so that it is, or just don't align the unwanted template residues with your target sequence).
Ben Webb, Modeller Caretaker
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Modeller Caretaker -
Sehrish Batool