I'm trying to use homology modelling to find the structure of the N-terminus of a protein which is thought to contribute to its hetero-oligomeric structure. However, I can't find an x-ray structure to use as a template. I use blast to search for pdb structures but none of them seem to have solved the structure of this region even though it is in their sequence. Is there a way of filtering out structures which do not have this region solved? If not, what would be a good alternative to solve the structure computationally?
Well, apparently this particular fragment has not been solved using xray; which is quite common for flexible N-termini. Try blasting only the sequence of the N-terminus and see if there's anything similar that can be used as a template. If yes, use Rosetta, Modeller or anything similar.
Use a sensitive homology detection method such as HHpred:
https://toolkit.tuebingen.mpg.de/#/tools/hhpred
It also makes sense to do secondary structure prediction and, in the case of helical regions, the prediction of coiled coils:
https://toolkit.tuebingen.mpg.de/#/tools/quick2d
https://toolkit.tuebingen.mpg.de/#/tools/deepcoil
With the results of these methods, one can decide what to do next (homology or de novo modeling). Feel free to contact me.
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