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Bioinformatics Advance Access originally published online on September 30, 2008
Bioinformatics 2008 24(23):2782-2783; doi:10.1093/bioinformatics/btn510
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© The Author 2008. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

MSX-3D: a tool to validate 3D protein models using mass spectrometry

Michaël Heymann 1, David Paramelle 2, Gilles Subra 2, Eric Forest 3, Jean Martinez 2, Christophe Geourjon 1 and Gilbert Deléage 1,*

1Institut de Biologie et Chimie des Protéines (IBCP) UMR5086 CNRS, Université Lyon 1, IFR128 BioSciences Lyon-Gerland, 7 passage du Vercors 69367 Lyon cedex 07, 2Institut des Biomolécules Max Mousseron (IBMM), UMR5247 CNRS, Universités Montpellier 1 et 2, 15 avenue Charles Flahault, 34000 Montpellier and 3Protein Mass Spectrometry Laboratory, Institut de Biologie Structurale, UMR5075 CEA, CNRS, UJF, 41 rue Jules Horowitz, 38027 Grenoble Cedex 1, France

*To whom correspondence should be addressed.


  Abstract

Motivation: The technique of chemical cross-linking followed by mass spectrometry has proven to bring valuable information about the protein structure and interactions between proteic subunits. It is an effective and efficient way to experimentally investigate some aspects of a protein structure when NMR and X-ray crystallography data are lacking.

Results: We introduce MSX-3D, a tool specifically geared to validate protein models using mass spectrometry. In addition to classical peptides identifications, it allows an interactive 3D visualization of the distance constraints derived from a cross-linking experiment.

Availability: Freely available at http://proteomics-pbil.ibcp.fr

Contact: g.deleage{at}ibcp.fr

Associate Editor: Anna Tramontano

Received on May 26, 2008; revised on August 28, 2008; accepted on September 27, 2008

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