PMID: 15245321Jul 13, 2004Paper

Reconstruction of protein structures from a vectorial representation

Physical Review Letters
Markus PortoM Vendruscolo

Abstract

We show that the contact map of the native structure of globular proteins can be reconstructed starting from the sole knowledge of the contact map's principal eigenvector, and present an exact algorithm for this purpose. Our algorithm yields a unique contact map for all 221 globular structures of PDBselect25 of length N</=120. We also show that the reconstructed contact maps allow in turn for the accurate reconstruction of the three-dimensional structure. These results indicate that the reduced vectorial representation provided by the principal eigenvector of the contact map is equivalent to the protein structure itself. This representation is expected to provide a useful tool in bioinformatics algorithms for protein structure comparison and alignment, as well as a promising intermediate step towards protein structure prediction.

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Citations

Nov 4, 2004·Proteins·Ugo BastollaMichele Vendruscolo
Feb 22, 2005·Bioinformatics·Akira R Kinjo, Ken Nishikawa
Jul 9, 2010·Bioinformatics·Pietro Di LenaRita Casadio
May 19, 2011·Bioinformatics·Haim AshkenazyYossef Kliger
Nov 30, 2006·Nucleic Acids Research·Andreas Martin Lisewski, Olivier Lichtarge
Apr 24, 2008·Proceedings. Biological Sciences·Evandro Ferrada, Andreas Wagner
Apr 1, 2006·BMC Bioinformatics·Alessandro VulloGianluca Pollastri
Nov 2, 2007·BMC Bioinformatics·Florian TeichertMarkus Porto
Oct 31, 2006·Algorithms for Molecular Biology : AMB·Martin PaluszewskiPawel Winter
Dec 10, 2009·PLoS Computational Biology·R SathyapriyaMichael Lappe
Dec 19, 2007·Biochimie·Guilhem FaureAlexandre G de Brevern
Jul 20, 2012·Journal of Bioinformatics and Computational Biology·Brian OlsonAmarda Shehu
Feb 21, 2006·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·N Hamedani RadjaM R Ejtehadi
May 23, 2006·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Todd J Taylor, Iosif I Vaisman
Nov 18, 2005·The European Physical Journal. E, Soft Matter·J F Sadoc
Jul 23, 2008·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Sanzo Miyazawa, Akira R Kinjo
Oct 30, 2014·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Marco NavaMichele Parrinello
Oct 10, 2006·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Hai-Bo CaoKai-Ming Ho
Sep 21, 2011·Physical Review Letters·Fabio Pietrucci, Wanda Andreoni
Dec 21, 2011·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Katrin WolffMarkus Porto
Jan 14, 2011·Journal of Chemical Information and Modeling·Jeremy EsqueAlexandre G de Brevern

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