Hey, that's a great project. The current situation with ProteinBoxBot is not ideal. We don't want to create a separate template for every protein. I suppose they do that now to make the articles slightly shorter, but Wikidata will allow us to accomplish the same thing without the confusing extra templates and ultimately to synchronize the infobox data across different language Wikipedias. With Wikidata the idea is that you will eventually just be able to write {{GNF Protein box}} at the top of the protein article and you will get what you want. If you look at our current list of biology properties though, there are still some that need to be added to fully support protein box.