I'd like to try to reproduce the interdomain linker prediction (Prot Sci 2007 16:165-175) on a two-domain protein we're working on. We don't have the full structure (yet) to back-check but do have NMR data to cross-validate any results. Regarding the published method, I wasn't sure how to model the linker while keeping the individual domains internally rigid but allowed to translate/rotate.
Using rosetta3, if I model the linker as a loop, the two domains stay fixed in space, greatly restricting the linker folding. If I use the ab initio routine, how do I enter the protein domains?
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modeling loops between domains