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Wang, C1; Zhang, HC; Zheng, WM; Xu, D3,4; Zhu, JW; Wang, B; Ning, K5; Sun, SW; Li, SC; Bu, DB
FALCON@home: a high-throughput protein structure prediction server based on remote homologue recognition
Source PublicationBIOINFORMATICS
Language英语
KeywordINFORMATION
AbstractThe 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.
2016
Volume32Issue:3Pages:462-464
Subject AreaBiochemistry & Molecular Biology ; Biotechnology & Applied Microbiology ; Computer Science ; Mathematical & Computational Biology ; Mathematics
DOIhttp://dx.doi.org/10.1093/bioinformatics/btv581
Indexed BySCI
Funding OrganizationNational Basic Research Program of China [2012CB316502] ; National Nature Science Foundation of China [11175224, 11121403, 31270834, 61272318, 30870572, 61303161] ; National Institutes of Health of USA [R21/R33-GM078601, R01-GM100701] ; European Commission [306819]
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Document Type期刊论文
Identifierhttp://ir.itp.ac.cn/handle/311006/23139
Collection理论物理所科研产出_SCI论文
Affiliation1.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
Recommended Citation
GB/T 7714
Wang, C,Zhang, HC,Zheng, WM,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, C.,Zhang, HC.,Zheng, WM.,Xu, D.,Zhu, JW.,...&Bu, DB.(2016).FALCON@home: a high-throughput protein structure prediction server based on remote homologue recognition.BIOINFORMATICS,32(3),462-464.
MLA Wang, C,et al."FALCON@home: a high-throughput protein structure prediction server based on remote homologue recognition".BIOINFORMATICS 32.3(2016):462-464.
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