Please see http://arstechnica.com/science/2017/01/in-chemistry-computational-models-may-be-getting-worse/ and http://science.sciencemag.org/content/355/6320/49 for context. I do not know anything about how computational models in chemistry work, but I think that if the models used by Rosetta@home are a victim to this phenomenon that is causing many modern chemical models to fail that the ones used by Rosetta@home could be fixed.

The counterpoint to this is the consistently good results that Rosetta achieves in CASP. Since some of the CASP targets have been solved by methods such as X-ray crystallography, this means that they are correct, in the sense that they represent the true structure of the protein.

It then follows from this that if a "simulation" such as Rosetta is able to match the real structure accurately, it implies that it is not subject to the inaccuracies cited in those two articles.

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