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

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

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  • 1Department of Biology, Northeastern University, 360 Huntington Avenue, Boston, MA 02115, USA.

Abstract

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 http://mozart.bio.neu.edu/topofit/index.php.

PMID:
17065464
PMCID:
PMC1635338
DOI:
10.1093/nar/gkl809
[PubMed - indexed for MEDLINE]
Free PMC Article
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