Question

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.

(a) True

(b) False

The question was asked in semester exam.

This intriguing question comes from Ab Initio Protein Structural Prediction & Homology Modeling in section Protein Tertiary Structure Prediction of Bioinformatics

Answer 1

Right answer is (a) True

To explain: In these loop modeling and side chain modeling steps, potential energy calculations are applied to improve the model. However, this does not guarantee that the entire raw homology model is free of structural irregularities such as unfavorable bond angles, bond lengths, or close atomic contacts. There, this step is used. The goal of energy minimization is to relieve steric collisions and strains without significantly altering the overall structure.