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Performance Analysis and Optimization of Cyro-EM Structure Determination in RELION-2

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Advanced Computer Architecture (ACA 2018)

Part of the book series: Communications in Computer and Information Science ((CCIS,volume 908))

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Abstract

REgularised LIkelihood OptimisatioN (RELION) is one of the most popular softwares used in single particle cryo-EM structure determination. Although efforts have been made to optimize the workflow of RELION, the refinement step still remains as a bottleneck for our exploration of performance improvement. In this paper, we thoroughly analyze the cause of the performance bottleneck and propose corresponding optimization for performance speedup. The experiment results show that our approach achieves a speedup of 3.17\(\times \) without degrading the resolution.

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Acknowledgments

This work is supported by the National Key R&D Program of China (Grant No. 2016YFB1000304) and National Natural Science Foundation of China (Grant No. 61502019).

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Authors and Affiliations

  1. School of Computer Science and Engineering, Beihang University, Beijing, 100191, China

    Xin You, Hailong Yang, Zhongzhi Luan & Depei Qian

Authors
  1. Xin You
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  2. Hailong Yang
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  3. Zhongzhi Luan
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  4. Depei Qian
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Corresponding author

Correspondence to Hailong Yang .

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Editors and Affiliations

  1. Shanghai Jiao Tong University, Shanghai, China

    Chao Li

  2. National University of Defense Technology, Changsha, China

    Junjie Wu

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You, X., Yang, H., Luan, Z., Qian, D. (2018). Performance Analysis and Optimization of Cyro-EM Structure Determination in RELION-2. In: Li, C., Wu, J. (eds) Advanced Computer Architecture. ACA 2018. Communications in Computer and Information Science, vol 908. Springer, Singapore. https://doi.org/10.1007/978-981-13-2423-9_15

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  • DOI: https://doi.org/10.1007/978-981-13-2423-9_15

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  • Publisher Name: Springer, Singapore

  • Print ISBN: 978-981-13-2422-2

  • Online ISBN: 978-981-13-2423-9

  • eBook Packages: Computer ScienceComputer Science (R0)

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