Title: Prot-2S: a new python web tool for protein secondary structure studies

Authors: Cristian R. Munteanu, Alexandre L. Magalhaes

Addresses: Faculty of Science, REQUIMTE/University of Porto, Department of Chemistry, Rua Campo Alegre 687, 4169-007 Porto, Portugal. ' Faculty of Science, REQUIMTE/University of Porto, Department of Chemistry, Rua Campo Alegre 687, 4169-007 Porto, Portugal

Abstract: Prot-2S is a bioinformatics web application devised to analyse the protein chain secondary structures (2S) (http:/ /www.requimte.pt:8080/Prot-2S/). The tool is built on the RCSB Protein Data Bank PDB and DSSP application/files and includes calculation/graphical display of amino acid propensities in 2S motifs based on any user amino acid classification/code (for any particular protein chain list). The interface can calculate the 2S composition, display the 2S subsequences and search for DSSP non-standard residues and for pairs/triplets/quadruplets (amino acid patterns in 2S motifs). This work presents some Prot-2S applications showing its usefulness in protein research and as an e-learning tool as well.

Keywords: protein secondary structures; python online application; amino acid propensity; e-learning; Prot-2S; python web tools; electronic learning; online learning; bioinformatics; protein chain; amino acid patterns; 2S motifs.

DOI: 10.1504/IJBRA.2009.027513

International Journal of Bioinformatics Research and Applications, 2009 Vol.5 No.4, pp.402 - 416

Received: 19 Jun 2007
Accepted: 12 Jun 2008

Published online: 28 Jul 2009 *

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