Question

Which of the following is untrue about Sequence Alignment Step?

(a) Once the structure with the highest sequence similarity is identified as a template, the full-length sequences of the template and target proteins need to be realigned using refined alignment algorithms to obtain optimal alignment

(b) The realignment is the most critical step in homology modeling

(c) The realignment directly affects the quality of the final model

(d) Errors made in the alignment step can be corrected in the following modeling steps

I had been asked this question in a job interview.

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

Answer 1

Right choice is (d) Errors made in the alignment step can be corrected in the following modeling steps

Best explanation: Incorrect alignment at this stage leads to incorrect designation of homologous residues and therefore to incorrect structural models. Errors made in the alignment step cannot be corrected in the following modeling steps. Therefore, the best possible multiple alignment algorithms, such as Praline and T-Coffee should be used for this purpose.