TOPOFIT-DB, a database of protein structural alignments based on the TOPOFIT method

Nucleic Acids Res. 2007 Jan;35(Database issue):D317-21. doi: 10.1093/nar/gkl809. Epub 2006 Oct 25.


TOPOFIT-DB (T-DB) is a public web-based database of protein structural alignments based on the TOPOFIT method, providing a comprehensive resource for comparative analysis of protein structure families. The TOPOFIT method is based on the discovery of a saturation point on the alignment curve (topomax point) which presents an ability to objectively identify a border between common and variable parts in a protein structural family, providing additional insight into protein comparison and functional annotation. TOPOFIT also effectively detects non-sequential relations between protein structures. T-DB provides users with the convenient ability to retrieve and analyze structural neighbors for a protein; do one-to-all calculation of a user provided structure against the entire current PDB release with T-Server, and pair-wise comparison using the TOPOFIT method through the T-Pair web page. All outputs are reported in various web-based tables and graphics, with automated viewing of the structure-sequence alignments in the Friend software package for complete, detailed analysis. T-DB presents researchers with the opportunity for comprehensive studies of the variability in proteins and is publicly available at

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Databases, Protein*
  • Internet
  • Mathematical Computing
  • Structural Homology, Protein*
  • User-Computer Interface