I think it is fine if it is "effective". Really most of our physics is effective. So valid at a certain length scale. Fluid mechanics is very good, but it does

I think it is fine if it is "effective". Really most of our physics is effective. So valid at a certain length scale. Fluid mechanics is very good, but it does not describe it all in terms of quark interactions. Quantum field theories are also mostly effective. So as long as it is describing protein dynamics at some effective length scale that is fine. Obviously it does not know anything about quarks/electrons/etc etc.