You can call me naive, or you can read my papers. For example, https://www.nature.com/articles/nchem.1821 is a massive simulation of a GPCR that my team designed and ran. It's a similar idea to the Relay work (simulate the dynamics of the protein, make a markov model of the subsets with transition parameters) With that tech, we could easily implement computational mutagenesis. I agree 100% that protein engineering is a great technology and I wish we could do it rationally. But to be honest, none of my computational work can beat what Jim Wells did at Genentech in the late 90s (converting subtilisin to subtiligase through amino acid mutations).

Here's another paper I wrote, https://www.ncbi.nlm.nih.gov/pubmed/24265211 which demonstrates there was a systematic error in protein force field implementations; our work was a major breakthrough in improving structure prediction.

Also, being able to predict structures isn't sufficient to engineer protein function.

Please don't call people naive; especially if they are experts in their field.