A standalone tool to mine protein data bank (PDB) for secondary structural elements

Abstract

Detailed structural analyses of protein necessitate investigation at primary, secondary and tertiary levels, respectively. Analysis of protein secondary structures pave way for understanding the type of secondary structural elements involved (α-helices, β-strands etc.), the number and length of the respective elements and the amino acid sequences that encode the secondary structural elements. Here we present a standalone tool entitled “ExSer” which facilitates an automated extraction of the amino acid sequences that encode for the secondary structural regions of a protein from the protein data bank (PDB) file.