Question

In the pairwise energy based method, a protein sequence is searched for in a structural fold database to find the best matching structural fold using ______ criteria.

(a) sequence-based

(b) structure-based

(c) energy-based

(d) residue-based

I got this question in an interview.

My doubt is from Threading and Fold Recognition in section Protein Tertiary Structure Prediction of Bioinformatics

Answer 1

Right answer is (c) energy-based

Explanation: The detailed procedure involves aligning the query sequence with each structural fold in a fold library. The alignment is performed essentially at the sequence profile level using dynamic programming or heuristic approaches. Local alignment is often adjusted to get lower energy and thus better fitting. The adjustment can be achieved using algorithms such as double-dynamic programming.