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

doi:10.1016/j.jtbi.2016.03.025

CORC > 北京大学 > 生命科学学院

	Identification of WD40 repeats by secondary structure-aided profile-profile alignment
	Wang, Chuan ; Dong, Xiaobao ; Han, Lei ; Su, Xiao-Dong ; Zhang, Ziding ; Li, Jinyan ; Song, Jiangning
刊名	JOURNAL OF THEORETICAL BIOLOGY
	2016
关键词	WD40 repeat Profile-profile alignment Remote sequence homology Secondary structure prediction Bioinformatics CRYSTAL-STRUCTURE G-PROTEIN RECOGNITION DATABASE DOMAIN SUBUNIT SEARCH SYSTEM DIVERSITY HOMOLOGY
DOI	10.1016/j.jtbi.2016.03.025
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.; State Education Ministry of China [20120008110014]; National Natural Science Foundation of China [31471249, 61202167, 61303169]; Hundred Talents Program of the Chinese Academy of Sciences (CAS); SCI(E); PubMed; ARTICLE; cwang@carnegiescience.edu; yndxb@126.com; hanlei_45@126.com; xdsu@pku.edu.cn; zidingzhang@cau.edu.cn; Jinyan.Li@uts.edu.au; jiangning.song@monash.edu; 122-129; 398
语种	英语
内容类型	期刊论文
源URL	[http://ir.pku.edu.cn/handle/20.500.11897/434345]
专题	生命科学学院
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.
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.
MLA	Wang, Chuan,et al."Identification of WD40 repeats by secondary structure-aided profile-profile alignment".JOURNAL OF THEORETICAL BIOLOGY (2016).