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Title

 

 

 

 

 

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

 

Authors

 

Vignesh Dhandapani, Paul Daniel, Raja Natarajan, Balasubramanian Ponnusamy, Arul Loganathan*

 

Affiliation

 

Department of Plant Molecular Biology and Biotechnology, Centre for Plant Molecular Biology, Tamil Nadu Agricultural University, Coimbatore - 641 003, India

 

Email

 

arulsra@gmail.com

 

Article Type

 

Database

Date

 

Received April 10, 2009; Revised February 03, 2010; accepted March 03, 2010; published March 31, 2010

 

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.

 

Availability ExSer is freely downloadable from http://code.google.com/p/tool-exser/

Keywords

Protein structure, secondary structural elements, α-helix, β-strand

Citation

 

Vignesh et al. Bioinformation 4(9): 390-391 (2010)

 

Edited by

 

P. Kangueane

ISSN

 

0973-2063

 

Publisher

 

Biomedical Informatics

License

 

 

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.