Question

The procedure begins by measuring the orientation and distance of the anchor regions in the stems and searching PDB for segments of the same length that also match the above endpoint conformation.

(a) True

(b) False

I had been asked this question in an online interview.

Origin of the question is Ab Initio Protein Structural Prediction & Homology Modeling in chapter Protein Tertiary Structure Prediction of Bioinformatics

Answer 1

The correct choice is (a) True

To explain I would say: Usually, many different alternative segments that fit the endpoints of the stems are available. The best loop can be selected based on sequence similarity as well as minimal steric clashes with the neighboring parts of the structure. The conformation of the best matching fragments is then copied onto the anchoring points of the stems.