FALCON@home: a high-throughput protein structure prediction server based on remote homologue recognition

doi:10.1093/bioinformatics/btv581

	FALCON@home: a high-throughput protein structure prediction server based on remote homologue recognition
	Wang, Chao 1,2; Zhang, Haicang 1,2; Zheng, Wei-Mou 3; Xu, Dong 4,5; Zhu, Jianwei 1; Wang, Bing 1; Ning, Kang 6; Sun, Shiwei 1; Li, Shuai Cheng 7; Bu, Dongbo 1
	2016-02-01
发表期刊	BIOINFORMATICS
ISSN	1367-4803
卷号	32 期号:3 页码:462-464
摘要	The protein structure prediction approaches can be categorized into template-based modeling (including homology modeling and threading) and free modeling. However, the existing threading tools perform poorly on remote homologous proteins. Thus, improving fold recognition for remote homologous proteins remains a challenge. Besides, the proteome-wide structure prediction poses another challenge of increasing prediction throughput. In this study, we presented FALCON@home as a protein structure prediction server focusing on remote homologue identification. The design of FALCON@home is based on the observation that a structural template, especially for remote homologous proteins, consists of conserved regions interweaved with highly variable regions. The highly variable regions lead to vague alignments in threading approaches. Thus, FALCON@home first extracts conserved regions from each template and then aligns a query protein with conserved regions only rather than the full-length template directly. This helps avoid the vague alignments rooted in highly variable regions, improving remote homologue identification. We implemented FALCON@home using the Berkeley Open Infrastructure of Network Computing (BOINC) volunteer computing protocol. With computation power donated from over 20 000 volunteer CPUs, FALCON@home shows a throughput as high as processing of over 1000 proteins per day. In the Critical Assessment of protein Structure Prediction (CASP11), the FALCON@homebased prediction was ranked the 12th in the template-based modeling category. As an application, the structures of 880 mouse mitochondria proteins were predicted, which revealed the significant correlation between protein half-lives and protein structural factors.
DOI	10.1093/bioinformatics/btv581
收录类别	SCI
语种	英语
资助项目	National Basic Research Program of China[2012CB316502] ; National Nature Science Foundation of China[11175224] ; National Nature Science Foundation of China[11121403] ; National Nature Science Foundation of China[31270834] ; National Nature Science Foundation of China[61272318] ; National Nature Science Foundation of China[30870572] ; National Nature Science Foundation of China[61303161] ; National Institutes of Health of USA[R21/R33-GM078601] ; National Institutes of Health of USA[R01-GM100701] ; European Commission[306819]
WOS研究方向	Biochemistry & Molecular Biology ; Biotechnology & Applied Microbiology ; Computer Science ; Mathematical & Computational Biology ; Mathematics
WOS类目	Biochemical Research Methods ; Biotechnology & Applied Microbiology ; Computer Science, Interdisciplinary Applications ; Mathematical & Computational Biology ; Statistics & Probability
WOS记录号	WOS:000370203000023
出版者	OXFORD UNIV PRESS
引用统计	被引频次：25[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://119.78.100.204/handle/2XEOYT63/8719
专题	中国科学院计算技术研究所期刊论文_英文
通讯作者	Li, Shuai Cheng; Bu, Dongbo
作者单位	1.Chinese Acad Sci, Inst Comp Technol, Key Lab Intelligent Informat Proc, Beijing, Peoples R China 2.Univ Chinese Acad Sci, Beijing, Peoples R China 3.Chinese Acad Sci, Inst Theoret Phys, Beijing 100080, Peoples R China 4.Univ Missouri, Dept Comp Sci, Columbia, MO 65211 USA 5.Univ Missouri, Christopher S Bond Life Sci Ctr, Columbia, MO 65211 USA 6.Huazhong Univ Sci & Technol, Coll Life Sci, Wuhan 430074, Peoples R China 7.City Univ Hong Kong, Dept Comp Sci, Kowloon, Hong Kong, Peoples R China
推荐引用方式 GB/T 7714	Wang, Chao,Zhang, Haicang,Zheng, Wei-Mou,et al. FALCON@home: a high-throughput protein structure prediction server based on remote homologue recognition[J]. BIOINFORMATICS,2016,32(3):462-464.
APA	Wang, Chao.,Zhang, Haicang.,Zheng, Wei-Mou.,Xu, Dong.,Zhu, Jianwei.,...&Bu, Dongbo.(2016).FALCON@home: a high-throughput protein structure prediction server based on remote homologue recognition.BIOINFORMATICS,32(3),462-464.
MLA	Wang, Chao,et al."FALCON@home: a high-throughput protein structure prediction server based on remote homologue recognition".BIOINFORMATICS 32.3(2016):462-464.