Identification of WD40 repeats by secondary structure-aided profile-profile alignment

CORC > 天津工业生物技术研究所 > 结构生物信息学和整合系统生物学实验室宋江宁 > 期刊论文

	Identification of WD40 repeats by secondary structure-aided profile-profile alignment
	Wang, Chuan 1,2; Dong, Xiaobao 1; Han, Lei 3; Su, Xiao-Dong 4,5; Zhang, Ziding 1; Li, Jinyan 6,7; Song, Jiangning 8,9,10,11,12
刊名	JOURNAL OF THEORETICAL BIOLOGY
	2016-06-07
卷号	398 期号:398 页码:122-129
关键词	WD40 repeat Profile-profile alignment Remote sequence homology Secondary structure prediction Bioinformatics
英文摘要	A WD40 protein typically contains four or more repeats of similar to 40 residues ended with the Trp-Asp dipeptide, which folds into beta-propellers with four beta strands in each repeat. They often function as scaffolds for protein-protein interactions and are involved in numerous fundamental biological processes. Despite their important functional role, the "velcro" closure of WD40 propellers and the diversity of WD40 repeats make their identification a difficult task. Here we develop a new WD40 Repeat Recognition method (WDRR), which uses predicted secondary structure information to generate candidate repeat segments, and further employs a profile-profile alignment to identify the correct WD40 repeats from candidate segments. In particular, we design a novel alignment scoring function that combines dot product and BLOSUM62, thereby achieving a great balance of sensitivity and accuracy. Taking advantage of these strategies, WDRR could effectively reduce the false positive rate and accurately identify more remote homologous WD40 repeats with precise repeat boundaries. We further use WDRR to re-annotate the Pfam families in the beta-propeller clan (CL0186) and identify a number of WD40 repeat proteins with high confidence across nine model organisms. The WDRR web server and the datasets are available at http://protein.cau.edu.cn/wdrr/. (C) 2016 Elsevier Ltd. All rights reserved.
WOS标题词	Science & Technology ; Life Sciences & Biomedicine
类目[WOS]	Biology ; Mathematical & Computational Biology
研究领域[WOS]	Life Sciences & Biomedicine - Other Topics ; Mathematical & Computational Biology
关键词[WOS]	CRYSTAL-STRUCTURE ; G-PROTEIN ; RECOGNITION ; DATABASE ; DOMAIN ; SUBUNIT ; SEARCH ; SYSTEM ; DIVERSITY ; HOMOLOGY
收录类别	SCI
语种	英语
WOS记录号	WOS:000375357400013
内容类型	期刊论文
源URL	[http://124.16.173.210/handle/834782/2260]
专题	天津工业生物技术研究所_结构生物信息学和整合系统生物学实验室宋江宁_期刊论文
作者单位	1.China Agr Univ, Coll Biol Sci, State Key Lab Agrobiotechnol, Beijing 100193, Peoples R China 2.Carnegie Inst Sci, Dept Plant Biol, 290 Panama St, Stanford, CA 94305 USA 3.Tianjin Med Univ, Canc Inst & Hosp, Natl Clin Res Ctr Canc, Ctr Canc Mol Diag, Tianjin, Peoples R China 4.Peking Univ, Sch Life Sci, State Key Lab Prot & Plant Gene Res, Beijing 100871, Peoples R China 5.Peking Univ, Sch Life Sci, Biodynam Opt Imaging Ctr BIOPIC, Beijing 100871, Peoples R China 6.Univ Technol Sydney, Adv Analyt Inst, 81 Broadway, Sydney, NSW 2007, Australia 7.Univ Technol Sydney, Ctr Hlth Technol, 81 Broadway, Sydney, NSW 2007, Australia 8.Chinese Acad Sci, Tianjin Inst Ind Biotechnol, Natl Engn Lab Ind Enzymes, Tianjin 300308, Peoples R China 9.Chinese Acad Sci, Tianjin Inst Ind Biotechnol, Key Lab Syst Microbial Biotechnol, Tianjin 300308, Peoples R China 10.Monash Univ, Fac Med, Biomed Discovery Inst, Infect & Immun Program, Melbourne, Vic 3800, Australia
推荐引用方式 GB/T 7714	Wang, Chuan,Dong, Xiaobao,Han, Lei,et al. Identification of WD40 repeats by secondary structure-aided profile-profile alignment[J]. JOURNAL OF THEORETICAL BIOLOGY,2016,398(398):122-129.
APA	Wang, Chuan.,Dong, Xiaobao.,Han, Lei.,Su, Xiao-Dong.,Zhang, Ziding.,...&Song, Jiangning.(2016).Identification of WD40 repeats by secondary structure-aided profile-profile alignment.JOURNAL OF THEORETICAL BIOLOGY,398(398),122-129.
MLA	Wang, Chuan,et al."Identification of WD40 repeats by secondary structure-aided profile-profile alignment".JOURNAL OF THEORETICAL BIOLOGY 398.398(2016):122-129.