Bioinformatics Vol. 16 no. 6 2000
Pages 520-526
© 2000 Oxford University Press
Original Paper |
Quick selection of representative protein chain sets based on customizable requirements
1 Parallel Application TRC Laboratory, Real
World Computing Partnership, Tsukuba Mitsui Building 1-6-1
Takezono, Tsukuba-shi Ibaraki 305-0032, Japan
2 Department of Informatics and Mathematical
Science, Graduate School of Engineering Science, Osaka University,
1-3 Machikaneyama, Toyonaka-shi Osaka 560-8531, Japan
Received on October 22, 1999
; accepted on February 3, 2000
Motivation: Protein structure classification has been recognized as one of the most important research issues in protein structure analysis. A substantial number of methods for the classification have been proposed, and several databases have been constructed using these methods. Since some proteins with very similar sequences may exhibit structural diversities, we have proposed PDB-REPRDB: a database of representative protein chains from the Protein Data Bank (PDB), which strategy of selection is based not only on sequence similarity but also on structural similarity. Forty-eight representative sets whose similarity criteria were predetermined were made available over the World Wide Web (WWW). However, the sets were insufficient in number to satisfy users researching protein structures by various methods.
Result: We have improved the system for PDB-REPRDB so that the user may obtain a quick selection of representative chains from PDB. The selection of representative chains can be dynamically configured according to the user’s requirement. The WWW interface provides a large degree of freedom in setting parameters, such as cut-off scores of sequence and structural similarity. This paper describes the method we use to classify chains and select the representatives in the system. We also describe the interface used to set the parameters.
Availability: The system for PDB-REPRDB is available at the PAPIA WWW server (http://www.rwcp.or.jp/papia/).
Contact: noguchi{at}trc.rwcp.or.jp
* To whom correspondence should be addressed.
3 Present address: Information Processing Systems Department, NKK Corporation, 1-1-2 Marunouchi, Chiyoda-ku, Tokyo 100-8202, Japan
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