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Bioinformatics Advance Access published online on April 19, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti458
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© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oupjournals.org
Received July 10, 2004
Revised January 24, 2005
Accepted April 18, 2005

Applications note

A web-based three-dimensional protein retrieval system by matching visual similarity

Jeng-Sheng Yeh 1*, Ding-Yun Chen 1, Bing-Yu Chen 2, and Ming Ouhyoung 3

1 Department of Computer Science and Information Engineering, National Taiwan University, Taipei 106, Taiwan
2 Department of Information Management, National Taiwan University, Taipei 106, Taiwan
3 Department of Computer Science and Information Engineering, National Taiwan University, Taipei 106, Taiwan; Graduate Institute of Network and Multimedia, National Taiwan University, Taipei 106, Taiwan

* To whom correspondence should be addressed.
Jeng-Sheng Yeh, E-mail: jsyeh{at}cmlab.csie.ntu.edu.tw


  Abstract

Summary: A web-based three-dimensional (3D) protein retrieval system is available for protein structure data including all PDB and FSSP dataset. In this system, we use a visual-based matching method to compare the protein structure from multiple viewpoints. It takes less than three seconds for each query with 90% accuracy on the average.

Availability: The web-based query interface and downloadable files can be accessed via http://3d.csie.ntu.edu.tw/ProteinRetrieval/.

Supplementary information: Further details of the proposed method are available at http://graphics.csie.ntu.edu.tw/~jsyeh/3Dprotein/.


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