G Labesse1, J Mornon. 1. Systèmes Moléculaires et Biologie Structurale, Laboratoire de Minéralogie-Cristallographie, Universités Paris, Cedex, France.
Abstract
MOTIVATION: 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. RESULTS: 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. AVAILABILITY: TITO is available by anonymous ftp at: ftp://lmcp.jussieu. fr/pub/tito CONTACT: labesse@lmcp.jussieu.fr SUPPLEMENTARY INFORMATION: http://www.lmcp.jussieu.fr/ approximately labesse/TITO/TITO.html
MOTIVATION: 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. RESULTS: 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. AVAILABILITY: TITO is available by anonymous ftp at: ftp://lmcp.jussieu. fr/pub/tito CONTACT: labesse@lmcp.jussieu.fr SUPPLEMENTARY INFORMATION: http://www.lmcp.jussieu.fr/ approximately labesse/TITO/TITO.html
Authors: Evangelia D Kouri; Nikolaos E Labrou; Spiros D Garbis; Katerina I Kalliampakou; Catalina Stedel; Maria Dimou; Michael K Udvardi; Panagiotis Katinakis; Emmanouil Flemetakis Journal: Plant Physiol Date: 2009-04-29 Impact factor: 8.340