My interest protein has 5 domains. A crystal structure with 3 domains together (A.pdb) is available. The other 2 domains crystal structure is available individually (B.pdb, C.pdb). Should I model the protein using multiple templates option and energy minimize it or should I dock the other domains (A.pdb with B.pdb and the resultant with C.pdb) and then energy minimize it for my further analysis
The result you get will be one of the million possibilities. Unless you have some distance restraints between inter-domain residues obtained via crosslinking or other studies, it may not be meaningful to proceed.
Yes, I agree with Dr. Thiyagarajan. Multiple possibilities are there.
You may perform template modelling with Modeller, but the reliability will remain questionable!
Deep knowledge on that particular protein is required. Then you get the idea what to do.
Thanks.
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