Nucleic Acids Research Advance Access first published online on October 25, 2006
This version published online on November 16, 2006
Nucleic Acids Research, doi:10.1093/nar/gkl809
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© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Database Issue |
TOPOFIT-DB, a database of protein structural alignments based on the TOPOFIT method
Department of Biology, Northeastern University 360 Huntington Avenue, Boston, MA 02115, USA
*To whom correspondence should be addressed. Tel: +1 617 373 7048; Fax: +1 617 373 3724; Email: ilyin{at}neu.edu
Received August 14, 2006. Revised September 21, 2006. Accepted September 29, 2006.
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.
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors
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