Incremental threading optimization (TITO) to help alignment and modelling of remote homologues

Bioinformatics
G Labesse, J Mornon

Abstract

Protein sequence comparison has become a major tool for biologists. Various methods have been designed in order to reveal even remote homologies among proteins. Sequence analyses are powerful, but the lower the identity score, the more skill and time are required to perform them accurately. While necessary to confirm the sequence comparison through the potential of mean force, sequence alignment and molecular modelling are still tedious and time-consuming tasks. In order to help sequence threading onto known three-dimensional (3D) structures, we have developed a new program, named TITO (Tool for Incremental Threading Optimization), which uses a multiple alignment to validate and help the refinement of a sequence/structure comparison. It measures the compatibility of a family of related sequences with a known 3D structure. The coordinates of the common core are extracted, allowing further molecular modelling and 3D survey. TITO is available by anonymous ftp at: ftp://lmcp.jussieu. fr/pub/tito labesse@lmcp.jussieu.fr http://www.lmcp.jussieu.fr/ approximately labesse/TITO/TITO.html

Citations

Feb 13, 2001·Biochemical and Biophysical Research Communications·G LabesseJ M Bolla
Apr 13, 2011·Archives of Microbiology·Patricio Sobrero, Claudio Valverde
Jan 20, 2004·Trends in Biochemical Sciences·Martin Cohen-GonsaudGilles Labesse
Jun 25, 2002·Journal of Molecular Biology·Martin Cohen-GonsaudAnnaïk Quemard
Jul 19, 2003·European Journal of Biochemistry·Cristina GagyiAnne-Marie Gilles
Jun 8, 2004·Nucleic Acids Research·Jérôme DelaunayOunissa Aït-Ahmed
Aug 4, 2005·Nucleic Acids Research·Frédéric AllemandCiarán Condon
May 16, 2009·Nucleic Acids Research·Jean-Luc Pons, Gilles Labesse
Nov 26, 2002·Molecular Biology and Evolution·Charles ClaudianosSteven Whyard
May 1, 2009·Plant Physiology·Evangelia D KouriEmmanouil Flemetakis
Oct 17, 2002·Protein Science : a Publication of the Protein Society·Cosmin SaveanuAnne-Marie Gilles
May 23, 2001·Protein Science : a Publication of the Protein Society·H Munier-LehmannG Labesse
Apr 12, 2006·Eukaryotic Cell·Sylvie BriquetCatherine Vaquero
Dec 17, 2002·Molecular and Cellular Biology·Magali SiautChristine Conesa
Feb 7, 2002·Biochemical and Biophysical Research Communications·Fernando Rodrigues-Lima, Jean-Marie Dupret
Mar 29, 2000·Biochemical and Biophysical Research Communications·F LaurentP de Wit
May 27, 2014·Journal of Chemical Information and Modeling·Alban LepailleurSylvain Rault
Jan 11, 2007·Biopolymers·Fabienne DulinJean-Paul Mornon
Jun 16, 2006·The Plant Journal : for Cell and Molecular Biology·Laurence AlbarAlain Ghesquière
Jul 25, 2006·Proteins·Nicolás PalopoliGustavo Parisi
Jun 11, 2002·Biochemical and Biophysical Research Communications·Gilles LabesseOctavian Bârzu
Oct 27, 2004·Molecular and Biochemical Parasitology·Charlotte BoschetCatherine Vaquero
Jun 19, 2004·Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences·N E KatsosY D Clonis
Apr 19, 2012·Molecular Plant·Valeria R TurowskiDiego F Gomez-Casati
Sep 2, 2004·The Journal of Biological Chemistry·Aditi DasTapas K Hazra
Jan 15, 2003·The Journal of Biological Chemistry·Jean-Luc PonsMarc-André Delsuc
Jun 22, 2018·Journal of Integrative Bioinformatics·Alexandre MaesMarc Baaden
Sep 7, 2001·The Journal of Biological Chemistry·F DocagneD Vivien
Oct 16, 1999·European Journal of Biochemistry·C CarretA Gorenflot
May 31, 2003·The Journal of Biological Chemistry·Emmanuelle LaurineJean-Michel Verdier

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