What is in silico energy optimization?
Generally, energy optimization is done as iterative process with following steps repeating 


calculate forces of nuclei
move nuclei according forces known so final structure were less tense.


Most focus in science is focused on how first step is made, as choice of the second step does not affect final structure except pathological cases. 

The main difference is usually tied to computational capabilities of 'silica' available. Complexity of quantum mechanical computations usually grows as $O(n^3)$, $O(n^4)$ or even $O(e^n)$ where n is number of atoms of same type in system. So, the bigger system is, the 'worse' approximation is used. Biological systems are usually so large, that any sort of quantum mechanical computation is not an option at all, so "molecular mechanics/dynamics" approach is used, with empiric formulas of forces based on relative positions of atoms