ViTO: tool for refinement of protein sequence-structure alignments

Bioinformatics. 2004 Dec 12;20(18):3694-6. doi: 10.1093/bioinformatics/bth429. Epub 2004 Jul 22.


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.


Supplementary information:

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Computer Graphics*
  • Imaging, Three-Dimensional / methods
  • Models, Molecular*
  • Molecular Sequence Data
  • Protein Conformation
  • Proteins / analysis
  • Proteins / chemistry*
  • Sequence Alignment / methods*
  • Sequence Analysis, Protein / methods*
  • Sequence Homology, Amino Acid
  • Software*
  • Structure-Activity Relationship
  • User-Computer Interface*


  • Proteins