Prediction of membrane protein types in a hybrid space
文献类型：期刊论文
| 作者 | Jia, Peilin1,2; Qian, Ziliang1,2; Feng, Kaiyan5; Lu, Wencong7,8; Li, Yixue1,4,6; Cai, Yudong3 |
| 刊名 | Journal of proteome research
 |
| 出版日期 | 2008-03-01 |
| 卷号 | 7期号:3页码:1131-1137 |
| 关键词 | Membrane protein Nearest neighbor algorithm Feature selection |
| ISSN号 | 1535-3893 |
| DOI | 10.1021/pr700715c |
| 通讯作者 | Li, yixue(yxli@sibs.ac.cn) |
| 英文摘要 | Prediction of the types of membrane proteins is of great importance both for genome-wide annotation and for experimental researchers to understand proteins' functions. we describe a new strategy for the prediction of the types of membrane proteins using the nearest neighbor algorithm. we introduced a bipartite feature space consisting of two kinds of disjoint vectors, proteins' domain profile and proteins' physiochemical characters. jackknife cross validation test shows that a combination of both features greatly improves the prediction accuracy. furthermore, the contribution of the physiochemical features to the classification of membrane proteins has also been explored using the feature selection method called "mrmr" (minimum redundancy, maximum relevance) (ieee trans. pattern anal. mach. intell. 2005, 27 (8), 1226-1238). a more compact set of features that are mostly contributive to membrane protein classification are obtained. the analyses highlighted both hydrophobicity and polarity as the most important features. the predictor with 56 most contributive features achieves an acceptable prediction accuracy of 87.02%. online prediction service is available freely on our web site http://pcal.biosino.org/transmembraneproteinclassification.html. |
| WOS关键词 | FUNCTIONAL DOMAIN COMPOSITION ; SUPPORT VECTOR MACHINES ; AMINO-ACID-COMPOSITION ; CLASSIFICATION ; RECOGNITION ; INFORMATION ; TOPOLOGY ; FOLD |
| WOS研究方向 | Biochemistry & Molecular Biology |
| WOS类目 | Biochemical Research Methods |
| 语种 | 英语 |
| WOS记录号 | WOS:000253825100028 |
| 出版者 | AMER CHEMICAL SOC |
| URI标识 | http://www.irgrid.ac.cn/handle/1471x/2386991 |
| 专题 | 中国科学院大学 |
| 通讯作者 | Li, Yixue |
| 作者单位 | 1.Chinese Acad Sci, Shanghai Inst Biol Sci, Key Lab Mol Syst Biol, Bioinformat Ctr, Shanghai 200031, Peoples R China 2.Chinese Acad Sci, Grad Sch, Beijing 100039, Peoples R China 3.Chinese Acad Sci, CAS MPG Partner Inst Computat Biol, Shanghai Inst Biol Sci, Beijing 100864, Peoples R China 4.Shanghai Ctr Bioinformat Technol, Shanghai 200235, Peoples R China 5.Univ Manchester, Div Imaging Sci & Biomed Engn, Manchester M13 9PT, Lancs, England 6.Shanghai Jiao Tong Univ, Coll Life Sci & Biotechnol, Shanghai, Peoples R China 7.Shanghai Univ, Dept Chem, Coll Sci, Shanghai 200444, Peoples R China 8.Shanghai Univ, Sch Mat Sci & Engn, Shanghai 200444, Peoples R China |
| 推荐引用方式 GB/T 7714 | Jia, Peilin,Qian, Ziliang,Feng, Kaiyan,et al. Prediction of membrane protein types in a hybrid space[J]. Journal of proteome research,2008,7(3):1131-1137. |
| APA | Jia, Peilin,Qian, Ziliang,Feng, Kaiyan,Lu, Wencong,Li, Yixue,&Cai, Yudong.(2008).Prediction of membrane protein types in a hybrid space.Journal of proteome research,7(3),1131-1137. |
| MLA | Jia, Peilin,et al."Prediction of membrane protein types in a hybrid space".Journal of proteome research 7.3(2008):1131-1137. |
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来源：中国科学院大学
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