ViTO: tool for refinement of protein sequence-structure alignments.
ViTO is a graphical application, including an editor, of multiple sequence alignment and a three-dimensional (3D) structure viewer. It is possible to manipulate alignments containing hundreds of sequences and to display a dozen structures. ViTO can handle so-called 'multiparts' alignments to allow the visualization of complex structures (multi-chain proteins and/or small molecules and DNA) and the editing of the corresponding alignment. The 3D viewer and the alignment editor are connected together allowing rapid refinement of sequence-structure alignment by taking advantage of the immediate visualization of resulting insertions/deletions and strict conservations in their structural context. More generally, it allows the mapping of informations about the sequence conservation extracted from the alignment onto the 3D structures in a dynamic way. ViTO is also connected to two comparative modelling programs, SCWRL and MODELLER. These features make ViTO a powerful tool to characterize protein families and to optimize the alignments for comparative modelling.


BACKGROUND
http://bioserv.cbs.cnrs.fr/VITO/DOC/.


BACKGROUND
http://bioserv.cbs.cnrs.fr/VITO/DOC/index.html.
Catherinot
Vincent
V
Centre de Biochimie Structurale, INSERM U414, CNRS UMR5048, Université Montpellier 1 15, Avenue Charles Flahault 34060 Montpellier Cedex, France. catrino@cbs.cnrs.fr <catrino@cbs.cnrs.fr>
Labesse
Gilles
G
D000595:Amino Acid Sequence; D003196:Computer Graphics; D021621:Imaging, Three-Dimensional / Q000379:methods; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011487:Protein Conformation; D011506:Proteins / Q000032:analysis / Q000737:chemistry*; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*; D017386:Sequence Homology, Amino Acid; D012984:Software; D013329:Structure-Activity Relationship; D014584:User-Computer Interface
D011506:Proteins