Prediction of palmitoylation sites using the composition of k-spaced amino acid pairs

doi:10.1093/protein/gzp055

CSpace > 应用数学研究所

	Prediction of palmitoylation sites using the composition of k-spaced amino acid pairs
	Wang, Xiao-Bo 1; Wu, Ling-Yun2 ; Wang, Yong-Cui 1; Deng, Nai-Yang 1
	2009-11-01
发表期刊	PROTEIN ENGINEERING DESIGN & SELECTION
ISSN	1741-0126
卷号	22 期号:11 页码:707-712
摘要	Palmitoylation is an important hydrophobic protein modification activity that participates many cellular processes, including signaling, neuronal transmission, membrane trafficking and so on. So it is an important problem to identify palmitoylated proteins and the corresponding sites. Comparing with the expensive and time-consuming biochemical experiments, the computational methods have attracted much attention due to their good performances in predicting palmitoylation sites. In this paper, we develop a novel automated computational method to perform this work. For a sequence segment in a given protein, the encoding scheme based on the composition of k-spaced amino acid pairs (CKSAAP) is introduced, and then the support vector machine is used as the predictor. The proposed prediction model CKSAAP-Palm outperforms the existing method CSS-Palm2.0 on both cross-validation experiments and some independent testing data sets. These results imply that our CKSAAP-Palm is able to predict more potential palmitoylation sites and increases research productivity in palmitoylation sites discovery. The corresponding software can be freely downloaded from http://www.aporc.org/doc/wiki/CKSAAP-Palm.
关键词	CKSAAP-Palm palmitoylated proteins palmitoylation support vector machine
DOI	10.1093/protein/gzp055
语种	英语
资助项目	National Natural Science Foundation of China[10631070] ; National Natural Science Foundation of China[60970091] ; Chinese Academy of Sciences ; [kjcx-yw-s7]
WOS研究方向	Biochemistry & Molecular Biology ; Biotechnology & Applied Microbiology
WOS类目	Biochemistry & Molecular Biology ; Biotechnology & Applied Microbiology
WOS记录号	WOS:000271109800008
出版者	OXFORD UNIV PRESS
引用统计
文献类型	期刊论文
条目标识符	http://ir.amss.ac.cn/handle/2S8OKBNM/8366
专题	应用数学研究所
通讯作者	Deng, Nai-Yang
作者单位	1.China Agr Univ, Coll Sci, Beijing 100083, Peoples R China 2.Chinese Acad Sci, Acad Math & Syst Sci, Inst Appl Math, Beijing 100190, Peoples R China
推荐引用方式 GB/T 7714	Wang, Xiao-Bo,Wu, Ling-Yun,Wang, Yong-Cui,et al. Prediction of palmitoylation sites using the composition of k-spaced amino acid pairs[J]. PROTEIN ENGINEERING DESIGN & SELECTION,2009,22(11):707-712.
APA	Wang, Xiao-Bo,Wu, Ling-Yun,Wang, Yong-Cui,&Deng, Nai-Yang.(2009).Prediction of palmitoylation sites using the composition of k-spaced amino acid pairs.PROTEIN ENGINEERING DESIGN & SELECTION,22(11),707-712.
MLA	Wang, Xiao-Bo,et al."Prediction of palmitoylation sites using the composition of k-spaced amino acid pairs".PROTEIN ENGINEERING DESIGN & SELECTION 22.11(2009):707-712.