Towards optimal alignment of protein structure distance matrices

Bioinformatics
Inken WohlersGunnar W Klau

Abstract

Structural alignments of proteins are important for identification of structural similarities, homology detection and functional annotation. The structural alignment problem is well studied and computationally difficult. Many different scoring schemes for structural similarity as well as many algorithms for finding high-scoring alignments have been proposed. Algorithms using contact map overlap (CMO) as scoring function are currently the only practical algorithms able to compute provably optimal alignments. We propose a new mathematical model for the alignment of inter-residue distance matrices, building upon previous work on maximum CMO. Our model includes all elements needed to emulate various scoring schemes for the alignment of protein distance matrices. The algorithm that we use to compute alignments is practical only for sparse distance matrices. Therefore, we propose a more effective scoring function, which uses a distance threshold and only positive structural scores. We show that even under these restrictions our approach is in terms of alignment accuracy competitive with state-of-the-art structural alignment algorithms, whereas it additionally either proves the optimality of an alignment or returns bounds on the optim...Continue Reading

References

Jul 5, 1989·Journal of Molecular Biology·W R Taylor, C A Orengo
Dec 15, 1982·Journal of Molecular Biology·O Gotoh
Sep 5, 1993·Journal of Molecular Biology·L Holm, C Sander
Oct 31, 1998·Protein Engineering·I N Shindyalov, P E Bourne
Nov 25, 1998·Protein Science : a Publication of the Protein Society·K MizuguchiJ P Overington
Aug 31, 2000·Journal of Molecular Biology·C NotredameJ Heringa
Aug 31, 2000·Protein Engineering·J Jung, B Lee
Jun 26, 2003·Nucleic Acids Research·Takeshi Kawabata
Jun 26, 2003·Nucleic Acids Research·Adam Zemla
Mar 24, 2004·Current Opinion in Chemical Biology·Alexander F YakuninCheryl H Arrowsmith
Apr 10, 2004·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Alberto CapraraBrian Walenz
Jul 21, 2004·Journal of Computational Chemistry·Eric F PettersenThomas E Ferrin
Aug 12, 2004·Proceedings of the National Academy of Sciences of the United States of America·Rachel Kolodny, Nathan Linial
Apr 26, 2005·Nucleic Acids Research·Yang Zhang, Jeffrey Skolnick
Oct 28, 2006·Nucleic Acids Research·Antonina AndreevaAlexey G Murzin
Jan 24, 2007·Bioinformatics·Fabian BirzeleRalf Zimmer
Apr 5, 2007·BMC Bioinformatics·Daron M StandleyHaruki Nakamura
Aug 4, 2007·BMC Structural Biology·Gabriele MayrPeter Lackner
Aug 9, 2007·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Wei Xie, Nikolaos V Sahinidis
Jan 16, 2008·PLoS Computational Biology·Matthew MenkeLenore Cowen
Mar 28, 2008·BMC Bioinformatics·David A PeltaMarcos Moreno Vega
Aug 12, 2008·Bioinformatics·Gergely CsabaRalf Zimmer
May 7, 2009·Bioinformatics·Jairo RochaSwagata Dasgupta
Jul 22, 2009·Protein Science : a Publication of the Protein Society·Christoph BerbalkPeter Lackner
Sep 8, 2009·Bioinformatics·Aleksandar Poleksic

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Citations

Jul 21, 2012·Journal of Biomolecular Structure & Dynamics·Jae-Kwan Kim, Deok-Soo Kim
May 4, 2012·Nucleic Acids Research·Inken WohlersGunnar W Klau
Aug 19, 2011·BMC Bioinformatics·Paweł Daniluk, Bogdan Lesyng
May 25, 2013·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Inken WohlersGunnar W Klau
Jun 9, 2015·Nature Methods·Yang Shen, Ad Bax
Aug 1, 2014·PLoS Computational Biology·Gabriel GonzalezWilliam F DeGrado
May 23, 2012·PLoS Computational Biology·M S Vijayabaskar, Saraswathi Vishveshwara
May 26, 2012·PloS One·Lakshmipuram Seshadri SwapnaNarayanaswamy Srinivasan
Jun 30, 2012·PloS One·Agnel Praveen JosephAlexandre G de Brevern
Mar 30, 2011·PloS One·Daqi TuMichael J Eck
Oct 4, 2011·PloS One·Erandi Lira-NavarreteRamon Hurtado-Guerrero
Oct 17, 2013·PloS One·Alexander LemakCheryl H Arrowsmith
Apr 28, 2010·PLoS Computational Biology·Narcis Fernandez-FuentesAndras Fiser
Dec 5, 2014·PLoS Computational Biology·Hua ChengNick V Grishin

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