Zhou Fengfeng, Xue Yu, Yao Xuebiao, Xu Ying
Computational Systems Biology Laboratory, Department of Biochemical and Molecular Biology and Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA.
Bioinformatics. 2006 Apr 1;22(7):894-6. doi: 10.1093/bioinformatics/btl013. Epub 2006 Jan 24.
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% and 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.
CSS-Palm is implemented in PHP/PERL+MySQL and can be freely accessed at http://bioinformatics.lcd-ustc.org/css_palm/
yaoxb@ustc.edu.cn; xuyn@bmb.uga.edu
Supplementary data are available at Bionformatics online.
棕榈酰化是一种重要的蛋白质翻译后脂质修饰。与异戊二烯化和肉豆蔻酰化不同，棕榈酰化是一种可逆的共价修饰，可对多个复杂细胞系统进行动态调控。然而，体内或体外鉴定棕榈酰化位点通常既耗时又费力。因此，计算机预测有助于缩小可能的棕榈酰化位点范围，可用于指导进一步的实验设计。先前的研究表明，棕榈酰化位点没有独特的典型基序，因此我们推测真正的模式可能会受到具有不同特征的多个结构决定因素的异质性影响。基于这一假设，我们将已知的棕榈酰化位点分为三类，并根据BLOSUM62矩阵对查询肽与训练肽之间的相似性进行评分。我们已经实现了一个用于棕榈酰化位点预测的计算机程序，即棕榈酰化位点预测的聚类与评分策略（CSS-Palm）系统，发现该程序的预测性能令人鼓舞，刀切法验证结果呈高度阳性（截止分数为2.6时，灵敏度为82.16%，特异性为83.17%）。我们的分析表明，CSS-Palm可为棕榈酰化位点的研究提供一个强大而有效的工具。
CSS-Palm用PHP/PERL+MySQL实现，可通过http://bioinformatics.lcd-ustc.org/css_palm/免费访问。
yaoxb@ustc.edu.cn；xuyn@bmb.uga.edu
补充数据可在《生物信息学》在线获取。
