Ab initio structure prediction classically refers to structure prediction using NOTHING more than first-principles (i.e. physics). DE NOVO is a more general term that refers to the greater category of methods that do not use templates from homologous PDB structures. Since Rosetta uses fragments from existing PDB structures in order to guide the search in conjunction with energy functions, there is a semantic argument as to WHETHER it is truly "ab initio" (although the same could be said for any statistically derived energy function). Long story short: call it what you WANT, but be prepared for a debate!

Ab initio structure prediction classically refers to structure prediction using nothing more than first-principles (i.e. physics). De Novo is a more general term that refers to the greater category of methods that do not use templates from homologous PDB structures. Since Rosetta uses fragments from existing PDB structures in order to guide the search in conjunction with energy functions, there is a semantic argument as to whether it is truly "ab initio" (although the same could be said for any statistically derived energy function). Long story short: call it what you want, but be prepared for a debate!