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PEDS Advance Access originally published online on August 27, 2008
Protein Engineering Design and Selection 2008 21(11):639-644; doi:10.1093/protein/gzn039
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© The Author 2008. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oxfordjournals.org

Methods

CSS-Palm 2.0: an updated software for palmitoylation sites prediction

Jian Ren1, Longping Wen1, Xinjiao Gao1, Changjiang Jin1, Yu Xue1,2 and Xuebiao Yao1,2

1Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science & Technology of China, Hefei, Anhui 230027, China

2 To whom correspondence should be addressed. E-mail: yaoxb{at}ustc.edu.cn (Y.X.)/xueyu{at}ustc.edu.cn (X.Y.)

Protein palmitoylation is an essential post-translational lipid modification of proteins, and reversibly orchestrates a variety of cellular processes. Identification of palmitoylated proteins with their sites is the foundation for understanding molecular mechanisms and regulatory roles of palmitoylation. Contrasting to the labor-intensive and time-consuming experimental approaches, in silico prediction of palmitoylation sites has attracted much attention as a popular strategy. In this work, we updated our previous CSS-Palm into version 2.0. An updated clustering and scoring strategy (CSS) algorithm was employed with great improvement. The leave-one-out validation and 4-, 6-, 8- and 10-fold cross-validations were adopted to evaluate the prediction performance of CSS-Palm 2.0. Also, an additional new data set not included in training was used to test the robustness of CSS-Palm 2.0. By comparison, the performance of CSS-Palm was much better than previous tools. As an application, we performed a small-scale annotation of palmitoylated proteins in budding yeast. The online service and local packages of CSS-Palm 2.0 were freely available at: http://bioinformatics.lcd-ustc.org/css_palm.

Keywords: clustering and scoring strategy/CSS-Palm/palmitoylated proteins/palmitoylation

Received March 27, 2008; revised June 16, 2008; accepted June 20, 2008.


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Home page
 Protein Eng Des SelHome page
X.-B. Wang, L.-Y. Wu, Y.-C. Wang, and N.-Y. Deng
Prediction of palmitoylation sites using the composition of k-spaced amino acid pairs
Protein Eng. Des. Sel., November 1, 2009; 22(11): 707 - 712.
[Abstract] [Full Text] [PDF]


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