Question

Energy minimization has to be used with caution because excessive energy minimization often moves residues away from their correct positions.

(a) True

(b) False

The question was asked during an online interview.

The query is from Ab Initio Protein Structural Prediction & Homology Modeling in portion Protein Tertiary Structure Prediction of Bioinformatics

Answer 1

The correct option is (a) True

To explain: Only limited energy minimization is recommended (a few hundred iterations) to remove major errors, such as short bond distances and close atomic clashes. Key conserved residues and those involved in cofactor binding have to be restrained if necessary during the process.