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Bioinformatics Advance Access originally published online on March 30, 2007
Bioinformatics 2007 23(11):1429-1430; doi:10.1093/bioinformatics/btm124
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© The Author 2007. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

PROTMAP2D: visualization, comparison and analysis of 2D maps of protein structure

Michal J. Pietal , Irina Tuszynska and Janusz M. Bujnicki *

Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology,Trojdena 4, 02-109 Warsaw, Poland

*To whom correspondence should be addressed.


  Abstract

Motivation: Protein structure comparison is a fundamental problem in structural biology and bioinformatics. Two-dimensional maps of distances between residues in the structure contain sufficient information to restore the 3D representation, while maps of contacts reveal characteristic patterns of interactions between secondary and super-secondary structures and are very attractive for visual analysis. The overlap of 2D maps of two structures can be easily calculated, providing a sensitive measure of protein structure similarity. PROTMAP2D is a software tool for calculation of contact and distance maps based on user-defined criteria, quantitative comparison of pairs or series of contact maps (e.g. alternative models of the same protein, model versus native structure, different trajectories from molecular dynamics simulations, etc.) and visualization of the results.

Availability: PROTMAP2D for Windows / Linux / MacOSX is freely available for academic users from http://genesilico.pl/protmap2d.htm

Contact: iamb{at}genesilico.pl

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Prof. Martin Bishop

Received on November 11, 2006; accepted on March 25, 2007

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[Abstract] [Full Text] [PDF]


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