I have a protein which has two chains each contains 422 residues, both chains are identical. I want to model this protein but the target sequence which I have contains more than 850 residues. When I combined the two chain residues as a single chain and aligned them with the target sequence it got aligned with the whole 850 residues target sequence and showed 56% identity. I want to model this two chains template protein into a single chain using my target sequence. How can i do it? Any suggestions?.
Perhaps I assume too much, but this is what I think you are saying. You have two identical chains which will preferentially match up with the same part of an 850 residue chain. I assume that you want to see where in the remainder of the 850 residue chain the second short chain should match up, given that the primary matching site is already busy with the first short chain. You get a high degree of homology in the first pairing, but the subsequent section of the long chain is not a good match. Would it be presumptious to suggest that you truncate N-terminus of the long chain just C-ward of the end of the high homology region? Of course, my assumptions about what you are trying to do may be completely off. Please clue me in if they are.
Go for single chain modeling of your protein at a time, as both the chains are identical. If your protein is a homodimer, go for protein-protein docking to get a homodimer model. Superimpose the modeled homodimer structure with the template to check RMSD.
Scott Helms when I took the sequence from both the chains i mean the total residues were 844 and aligned with the 850 residue chain using clustalW2 it got aligned well and shows 56% identity. but the question is when i go for modelling using modeller 9.12 I could do only two chain modelling but i want to model a 850 residues protein as a single chain, using the above two chain template protein. How can i do it.
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