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Nucleic Acids Research Advance Access published online on June 6, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm353
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© 2007 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.

Web Server Issue

iPDA: integrated protein disorder analyzer

Chung-Tsai Su1, Chien-Yu Chen2,* and Chen-Ming Hsu3

1Department of Computer Science and Information Engineering, National Taiwan University, Taipei 106, Taiwan, 2Department of Bio-Industrial Mechatronics Engineering, National Taiwan University, Taipei, 106, Taiwan and 3Department of Computer Science and Engineering, Yuan Ze University, Chung-Li, 320, Taiwan, ROC

*To whom correspondence should be addressed. Tel: +886-2-33665334; Fax: +886-2-23627620; Email: cychen{at}mars.csie.ntu.edu.tw

Received January 31, 2007. Revised April 18, 2007. Accepted April 23, 2007.

This article presents a web server iPDA, which aims at identifying the disordered regions of a query protein. Automatic prediction of disordered regions from protein sequences is an important problem in the study of structural biology. The proposed classifier DisPSSMP2 is different from several existing disorder predictors by its employment of position-specific scoring matrices with respect to physicochemical properties (PSSMP), where the physicochemical properties adopted here especially take the disorder propensity of amino acids into account. The web server iPDA integrates DisPSSMP2 with several other sequence predictors in order to investigate the functional role of the detected disordered region. The predicted information includes sequence conservation, secondary structure, sequence complexity and hydrophobic clusters. According to the proportion of the secondary structure elements predicted, iPDA dynamically adjusts the cutting threshold of determining protein disorder. Furthermore, a pattern mining package for detecting sequence conservation is embedded in iPDA for discovering potential binding regions of the query protein, which is really helpful to uncovering the relationship between protein function and its primary sequence. The web service is available at http://biominer.bime.ntu.edu.tw/ipda and mirrored at http://biominer.cse.yzu.edu.tw/ipda.


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