Spark-based parallel calculation of 3D fourier shell correlation for macromolecule structure local resolution estimation

doi:10.1186/s12859-020-03680-6

	Spark-based parallel calculation of 3D fourier shell correlation for macromolecule structure local resolution estimation
	Lue, Yongchun 1,2; Zeng, Xiangrui 3; Tian, Xinhui 1; Shi, Xiao 1; Wang, Hui 1; Zheng, Xiaohui 1,2; Liu, Xiaodong 1; Zhao, Xiaofang 1,2; Gao, Xin 4; Xu, Min 3
	2020-09-17
发表期刊	BMC BIOINFORMATICS
ISSN	1471-2105
卷号	21 页码:18
摘要	BackgroundResolution estimation is the main evaluation criteria for the reconstruction of macromolecular 3D structure in the field of cryoelectron microscopy (cryo-EM). At present, there are many methods to evaluate the 3D resolution for reconstructed macromolecular structures from Single Particle Analysis (SPA) in cryo-EM and subtomogram averaging (SA) in electron cryotomography (cryo-ET). As global methods, they measure the resolution of the structure as a whole, but they are inaccurate in detecting subtle local changes of reconstruction. In order to detect the subtle changes of reconstruction of SPA and SA, a few local resolution methods are proposed. The mainstream local resolution evaluation methods are based on local Fourier shell correlation (FSC), which is computationally intensive. However, the existing resolution evaluation methods are based on multi-threading implementation on a single computer with very poor scalability.ResultsThis paper proposes a new fine-grained 3D array partition method by key-value format in Spark. Our method first converts 3D images to key-value data (K-V). Then the K-V data is used for 3D array partitioning and data exchange in parallel. So Spark-based distributed parallel computing framework can solve the above scalability problem. In this distributed computing framework, all 3D local FSC tasks are simultaneously calculated across multiple nodes in a computer cluster. Through the calculation of experimental data, 3D local resolution evaluation algorithm based on Spark fine-grained 3D array partition has a magnitude change in computing speed compared with the mainstream FSC algorithm under the condition that the accuracy remains unchanged, and has better fault tolerance and scalability.ConclusionsIn this paper, we proposed a K-V format based fine-grained 3D array partition method in Spark to parallel calculating 3D FSC for getting a 3D local resolution density map. 3D local resolution density map evaluates the three-dimensional density maps reconstructed from single particle analysis and subtomogram averaging. Our proposed method can significantly increase the speed of the 3D local resolution evaluation, which is important for the efficient detection of subtle variations among reconstructed macromolecular structures.
关键词	3D local Fourier shell correlation 3D local resolution map Key-value data Spark 3D array partition
DOI	10.1186/s12859-020-03680-6
收录类别	SCI
语种	英语
资助项目	King Abdullah University of Science and Technology (KAUST) Office of Sponsored Research (OSR)[URF/1/2602-01] ; King Abdullah University of Science and Technology (KAUST) Office of Sponsored Research (OSR)[URF/1/3007-01] ; National Key R&D Program of China[2018YFB0904503] ; National Key R&D Program of China[2017YFB1002703] ; Key Research Program of Frontier Science of Chinese Academy of Sciences[QYZDB-SSW-SMC004] ; National Natural Science Foundation of China[61379082] ; National Natural Science Foundation of China[61672499] ; U.S. National Institutes of Health (NIH)[P41 GM103712] ; U.S. National Science Foundation (NSF)[DBI-1949629] ; Carnegie Mellon University's Center for Machine Learning and Health
WOS研究方向	Biochemistry & Molecular Biology ; Biotechnology & Applied Microbiology ; Mathematical & Computational Biology
WOS类目	Biochemical Research Methods ; Biotechnology & Applied Microbiology ; Mathematical & Computational Biology
WOS记录号	WOS:000573082700013
出版者	BMC
引用统计
文献类型	期刊论文
条目标识符	http://119.78.100.204/handle/2XEOYT63/15570
专题	中国科学院计算技术研究所期刊论文_英文
通讯作者	Lue, Yongchun; Xu, Min
作者单位	1.Chinese Acad Sci, Inst Comp Technol, Beijing, Peoples R China 2.Univ Chinese Acad Sci, Beijing, Peoples R China 3.Carnegie Mellon Univ, Sch Comp Sci, Computat Biol Dept, Pittsburgh, PA 15213 USA 4.King Abdullah Univ Sci & Technol KAUST, Computat Biosci Res Ctr CBRC, Comp Elect & Math Sci & Engn CEMSE Div, Thuwal, Saudi Arabia
推荐引用方式 GB/T 7714	Lue, Yongchun,Zeng, Xiangrui,Tian, Xinhui,et al. Spark-based parallel calculation of 3D fourier shell correlation for macromolecule structure local resolution estimation[J]. BMC BIOINFORMATICS,2020,21:18.
APA	Lue, Yongchun.,Zeng, Xiangrui.,Tian, Xinhui.,Shi, Xiao.,Wang, Hui.,...&Xu, Min.(2020).Spark-based parallel calculation of 3D fourier shell correlation for macromolecule structure local resolution estimation.BMC BIOINFORMATICS,21,18.
MLA	Lue, Yongchun,et al."Spark-based parallel calculation of 3D fourier shell correlation for macromolecule structure local resolution estimation".BMC BIOINFORMATICS 21(2020):18.