Abstract
Detailed structural analysis of protein necessitates investigation at primary, secondary and tertiary levels, respectively. Insight into protein secondary structures pave way for understanding the type of secondary structural elements involved (α-helices, β-strands etc.), the amino acid sequence that encode the secondary structural elements, number of residues, length and, percentage composition of the respective elements in the protein. Here we present a standalone tool entitled "ExSer" which facilitate an automated extraction of the amino acid sequence that encode for the secondary structural regions of a protein from the protein data bank (PDB) file. ExSer is freely downloadable from http://code.google.com/p/tool-exser/
Highlights
Protein structures are determined by experimental methods which include NMR, X-ray and Electronic Microscopy
Protein Data Bank (PDB) is an internationally referred protein structure database, it comprises of the atomic coordinates of the three dimensional (3D) structure of proteins [2]
Information that are embedded in the PDB file such as the amino acid sequence of the secondary structural elements viz., α-helices and β-strands, is of significant interest to the scientific community
Summary
Protein structures are determined by experimental methods which include NMR, X-ray and Electronic Microscopy. Protein Data Bank (PDB) is an internationally referred protein structure database, it comprises of the atomic coordinates of the three dimensional (3D) structure of proteins [2]. Secondary structural information and atom positions are organized systematically in the PDB file enabling machine learning [4].
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