Skip Navigation



Bioinformatics Advance Access published online on January 24, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl013
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrow Supplementary Data
Right arrowOA All Versions of this Article:
22/7/894    most recent
btl013v1
Right arrow Comments: Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when Comments are posted
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Google Scholar
Right arrow Articles by Zhou, F.
Right arrow Articles by Xu, Y.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Zhou, F.
Right arrow Articles by Xu, Y.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received December 20, 2005
Revised January 19, 2006
Accepted January 20, 2006

Applications note

CSS-Palm: palmitoylation site prediction with a clustering and scoring strategy (CSS)

Fengfeng Zhou 1 {dagger}, Yu Xue 2 {dagger}, Xuebiao Yao 3, and Ying Xu 1 *

1 Computational Systems Biology Laboratory, Department of Biochemical and Molecular Biology and Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
2 Laboratory of Cellular Dynamics, Hefei National Laboratory for Physical Sciences, and the University of Science and Technology of China, Hefei, China 230027
3 Laboratory of Cellular Dynamics, Hefei National Laboratory for Physical Sciences, and the University of Science and Technology of China, Hefei, China 230027; Department of Physiology and Cancer Research Program, Morehouse School of Medicine, Atlanta, GA 30310; USA

* To whom correspondence should be addressed.
Ying Xu, E-mail: xyn{at}bmb.uga.edu


  Abstract

Palmitoylation is an important post-translational lipid modification of proteins. Unlike prenylation and myristoylation, palmitoylation is a reversible covalent modification, allowing for dynamic regulation of multiple complex cellular systems. However, in vivo or in vitro identification of palmitoylation sites is usually time-consuming and labor-intensive. So in silico predictions could help to narrow down the possible Palmitoylation sites, which can be used to guide further experimental design. Previous studies suggested that there is no unique canonical motif for palmitoylation sites, so we hypothesize that the bona fide pattern might be compromised by heterogeneity of multiple structural determinants with different features. Based on this hypothesis, we partition the known palmitoylation sites into three clusters and score the similarity between the query peptide and the training ones based on BLOSUM62 matrix. We have implemented a computer program for palmitoylation site prediction, Clustering and Scoring Strategy for Palmitoylation Sites Prediction (CSS-Palm) system, and found that the program's prediction performance is encouraging with highly positive Jack-Knife validation results (sensitivity 82.16% & specificity 83.17% for cut-off score 2.6). Our analyses indicate that CSS-Palm could provide a powerful and effective tool to studies of palmitoylation sites.

Availability: CSS-Palm is implemented in PHP/PERL+MySQL and can be freely accessed at http://bioinformatics.lcd-ustc.org/css_palm/.

Supplementary Information: The supplementary materials, including the details of the algorithm, could be visited from: http://bioinformatics.lcd-ustc.org/css_palm/faq.php

{dagger}The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.

Associate Editor: Martin Bishop


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


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]

Home page
 J. Biol. Chem.Home page
J. Claudinon, P. Gonnord, E. Beslard, M. Marchetti, K. Mitchell, C. Boularan, L. Johannes, P. Eid, and C. Lamaze
Palmitoylation of Interferon-{alpha} (IFN-{alpha}) Receptor Subunit IFNAR1 Is Required for the Activation of Stat1 and Stat2 by IFN-{alpha}
J. Biol. Chem., September 4, 2009; 284(36): 24328 - 24340.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
L. Tian, O. Jeffries, H. McClafferty, A. Molyvdas, I. C. M. Rowe, F. Saleem, L. Chen, J. Greaves, L. H. Chamberlain, H.-G. Knaus, et al.
Palmitoylation gates phosphorylation-dependent regulation of BK potassium channels
PNAS, December 30, 2008; 105(52): 21006 - 21011.
[Abstract] [Full Text] [PDF]

Home page
 Protein Eng Des SelHome page
J. Ren, L. Wen, X. Gao, C. Jin, Y. Xue, and X. Yao
CSS-Palm 2.0: an updated software for palmitoylation sites prediction
Protein Eng. Des. Sel., November 1, 2008; 21(11): 639 - 644.
[Abstract] [Full Text] [PDF]

Home page
 GENES CELLSHome page
K. Tsutsumi, M. Tomomura, T. Furuichi, and S.-i. Hisanaga
Palmitoylation-dependent endosomal localization of AATYK1A and its interaction with Src
Genes Cells, September 1, 2008; 13(9): 949 - 964.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.