Basic Applied Bioinformatics

CHAPTER 30Protein Structure Prediction Using Threading Method

CS Mukhopadhyay and HK Manku

School of Animal Biotechnology, GADVASU, Ludhiana

30.1 INTRODUCTION

Threading or fold recognition is the method for protein tertiary structure prediction, and is implemented when no significant homologs are searched. The underlying theory assumes the existence of a limited number of distinct protein folds. The threading method thus searches the structural analogs of the query sequence in a library of representative structures through comparative fold recognition. The threading approach relies on fitting the target peptide sequence to one or more entries of a library of protein structures (e.g., protein domains, peptide chains or conserved protein cores). The best fit is evaluated on the basis of an appropriate energy function (determined by a biocomputational algorithm) to determine the best possible templates. In this way, folds are recognized simultaneously, and the whole structure can be predicted.

30.2 OBJECTIVE

To predict the tertiary structure of a protein sequence using the fold recognition method.

30.3 PROCEDURE

3D structure prediction using the threading method is explained by using the RaptorX server:

1. Query submission: Submit a query sequence for protein structure prediction via the URL http://raptorx.uchicago.edu/StructurePrediction/predict/.
2. Click on “Submit a new job”.
3. Create a job identification title so that you can access your results page in the future.
4. Enter a valid ...