{Complexity}

Once we figure out the protein sequence, then how we can figure out its 3D structure?
There are two kinds of methods. Physical and empirical methods. The physical prediction methods are based on interactions between atoms and include molecular dynamics and energy minimization, whereas the empirical methods depend on the protein structures that have been already determined by experiments.
A comparative protein modeling method designed to find the most probable structure for a sequence given its alignment with related structures. 3D model is obtained by optimally satisfying spatial restraints derived from the alignment and expressed as probability density functions for the features restrained.

Evolution and Physics in comparative protein structure modeling.pdf
Comparative_Protein_Modeling.pdf