Question

Which of the following is untrue about Loop Modeling Step?

(a) In the sequence alignment for modeling, there are often regions caused by insertions and deletions producing gaps in sequence alignment

(b) In the sequence alignment for modeling, there are no regions producing gaps in sequence alignment

(c) The gaps cannot be directly modeled

(d) Loop modeling is required for closing the gaps requires

I had been asked this question by my college professor while I was bunking the class.

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

Answer 1

Right choice is (b) In the sequence alignment for modeling, there are no regions producing gaps in sequence alignment

To explain I would say: Closing the gaps requires loop modeling, which is a very difficult problem in homology modeling and is also a major source of error. Loop modeling can be considered a mini–protein modeling problem by itself. Unfortunately, there are no mature methods available that can model loops reliably. Currently, there are two main techniques used to approach the problem: the database searching method and the ab initio method.