Bioinformatics, Vol 14, 206-211, Copyright © 1998 by Oxford University Press
G Labesse and J Mornon
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
ARTICLES
Incremental threading optimization (TITO) to help alignment and modelling of remote homologues
Systemes Moleculaires et Biologie Structurale, Laboratoire de Mineralogie-Cristallographie, Universites Paris, Cedex, France.
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