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Bioinformatics Advance Access originally published online on June 24, 2004
Bioinformatics 2004 20(17):3277-3279; doi:10.1093/bioinformatics/bth367
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Bioinformatics vol. 20 issue 17 © Oxford University Press 2004; all rights reserved.

Applications Note

PTGL—a web-based database application for protein topologies

Patrick May 1, Stefan Barthel 2 and Ina Koch 2,*

1 BCB Junior Research Group, ZIB Berlin, Takustr.7, Berlin 14195, Germany and 2 Department of Bioinformatics, Technical University of Applied Sciences, Berlin, Seestrasse 64, 13347 Berlin Germany

Received on November 10, 2003; revised on May 17, 2004; accepted on June 4, 2004
Advance Access Publication June 24, 2004

Summary: Protein Topology Graph Library (PTGL) is a database application for the representation and retrieval of protein topologies. Protein topologies are based on a graph-theoretical protein model at secondary structure level. Different views on protein topology are given by four linear notations for their characterization. Protein topologies can be derived at different description levels considering {alpha}- and ß-structures. The on-line search tool is based on an object-relational database and provides a query browser for data interrogation by string patterns, keyword queries and sequence similarity. Protein topologies are represented both as schematic diagrams and as three-dimensional images.

Availability: http://sanaga.tfh-berlin.de/~ptgl/ptgl.html

Contact: ina.koch{at}tfh-berlin.de

* To whom correspondence should be addressed.


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