Before revision:  However, it remains a challenge to combine a classification scheme that describes a protein starting from its  secondary structures and often involves direct human involvement, with an atomary level Physics based approach where a protein is fundamentally viewed as not much more than an ensemble of mutually interacting carbon, hydrogen, oxygen and nitrogen atoms.
After revision:  However, it remains a challenge to combine a classification scheme that describes a protein starting from its URLanized secondary structures and often involves direct human involvement, with an atomary level Physics based approach where a protein is fundamentally viewed as not much more than an ensemble of mutually interacting carbon, hydrogen, oxygen and nitrogen atoms.