Question

Which of the following is untrue about template Selection Step?

(a) The first step in protein structural modeling is to select appropriate structural templates

(b) This forms the foundation for rest of the modeling process

(c) There is no use of heuristic alignment search programs

(d) The template selection involves searching the Protein Data Bank (PDB) for homologous proteins with determined structures

I had been asked this question in semester exam.

The doubt is from Ab Initio Protein Structural Prediction & Homology Modeling in chapter Protein Tertiary Structure Prediction of Bioinformatics

Answer 1

Correct choice is (c) There is no use of heuristic alignment search programs

To explain I would say: The search can be performed using a heuristic pair wise alignment search program such as BLAST or FASTA. However, the use of dynamic programming based search programs such as SEARCH or ScanPS can result in more sensitive search results. The relatively small size of the structural database means that the search time using the exhaustive method is still within reasonable limits, while giving a more sensitive result to ensure the best possible similarity hits.