In the step of Model Refinement Using Energy Function, the structural irregularities can be corrected by applying the energy minimization procedure on the entire model, which moves the atoms in such a way that the overall conformation has the lowest energy potential.

Tertiary protein structure prediction is computational elucidation of the three-dimensional structure of a protein for which experimentally determined structure is unavailable from its amino acid sequence.

Topic include: Ab Initio Protein Structural Prediction & Homology Modeling, & Threading and Fold Recognition.