Question

Which of the following is true about Gen Threader?

(a) It is a web-based program that uses a hybrid of the profile and pairwise energy methods

(b) It is a web-based program that uses profile methods only

(c) It is a web-based program that uses pairwise energy methods only

(d) The initial step is quite dissimilar to 3D-PSSM

The question was asked in exam.

The question is from Threading and Fold Recognition topic in division Protein Tertiary Structure Prediction of Bioinformatics

Answer 1

Correct choice is (a) It is a web-based program that uses a hybrid of the profile and pairwise energy methods

To elaborate: The initial step is similar to 3D-PSSM; the query protein sequence is subject to three rounds of PSI-BLAST. The resulting multiple sequence hits are used to generate a profile. Its secondary structure is predicted using PSIPRED. Both are used as input for threading computation based on a pairwise energy potential method. The threading results are evaluated using neural networks that combine energy potentials, sequence alignment scores, and length information to create a single score representing the relationship between the query and template proteins.