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How Do You Combine Fragments Of One Protein Modeled Separately?

I have found some templates for some sections of my protein whose structure I want to determine. I want to use homology modeling for those fragments and then ab initio for the other fragments. How do I combine the separate models to get one wholesome structure?

structure prediction homology

When you say structure, do you mean 3D structure (xray crystallography) or gene structure (start, internal, intron/exon boundaries, etc)?

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