Basic Applied Bioinformatics

CHAPTER 28Prediction of Secondary Structure of Protein

CS Mukhopadhyay and RK Choudhary

School of Animal Biotechnology, GADVASU, Ludhiana

28.1 INTRODUCTION

Secondary structures of a protein (e.g., α‐helix, β‐sheets, loops, and coils) are produced due to the patterns of hydrogen bonds between amino and carboxyl groups of the adjacent amino acids of the peptide backbone. The prediction of the secondary structure of proteins consists of a set of biocomputational approaches directed towards assigning the regions of local folding of protein (i.e., the secondary structure), based on the amino acid sequence (i.e., the primary structure).

28.2 OBJECTIVE

To predict the secondary structure of a given peptide molecule, using an online secondary structure prediction tool.

28.3 SECONDARY STRUCTURE PREDICTION USING ONLINE TOOL PSIPRED

28.3.1 Procedure

28.3.1.1 Download the amino acid sequence

Download a peptide sequence (e.g., taurine Keratin: NCBI protein Acc. No. Q148H4.1) from NCBI‐Protein (http://www.ncbi.nlm.nih.gov/protein/) or UniProt (http://www.uniprot.org/uniprot/) database, in FASTA format.

> Q148H4.1|BovineKeratin

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