Macromolecular Modeling Blog ™

The Rosetta macromolecular modeling suite has a very wide range of applications, and although installing and running Rosetta, becomes increasingly easier over the years, some non-experts would still prefer to run it over a comfortable to use web-server. We have assembled here the list of Rosetta applications for which such a web-server exists. Bookmark for future modeling tasks.

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Although numerous structures of peptide bound MHC-II molecules were solved, no one knows how does the peptide free MHC look like. Painter et al. elegantly use molecular dynamics to model the conformational changes upon peptide removal. Most interestingly a helix from the peptide binding domain adopts the binding mode of the antigen peptide. They successfully validate their model using antibodies and superantigens, predicted to differentially bind peptide-bound/free molecules according to their model. We take the validation one step further and propose mutations based on Painter’s model that would stabilize the free MHC. Will it work? Who will pick up the gauntlet?

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