Question

In Side Chain Refinement step, A side chain can be built by searching every possible conformation at every torsion angle of the side chain to select the one that has the lowest interaction energy with neighboring atoms.

(a) True

(b) False

The question was asked in exam.

My question is based upon Ab Initio Protein Structural Prediction & Homology Modeling topic in section Protein Tertiary Structure Prediction of Bioinformatics

Answer 1

Right option is (a) True

To elaborate: However, this approach is computationally prohibitive in most cases. In fact, most current side chain prediction programs use the concept of rotamers, which are favored side chain torsion angles extracted from known protein crystal structures. In prediction of side chain conformation, only the possible rotamers with the lowest interaction energy with nearby atoms are selected.