Skip to main content
SpringerLink
Log in
SpringerLink
Log in

Distributed Computation for Protein Structure Analysis

  • Conference paper
  • First Online:
Advances in Intelligent Networking and Collaborative Systems (INCoS 2018)

Part of the book series: Lecture Notes on Data Engineering and Communications Technologies ((LNDECT,volume 23))

  • 1006 Accesses

Abstract

To understand how proteins function it is crucial to understand the connection between their structure, flexibility and dynamics. In the field of bioinformatics and computational biology, there is a strong interest to develop software and computational tools that analyzes various properties of protein structures. The software we are using for protein flexibility and dynamics analysis generally assumes a single task, single thread environment. To more efficiently elucidate the function of proteins, we need to perform large-scale calculations on many structures. To improve computational speed of such large scale analysis, we decided to perform parallel distributed computation with the conventional software. We designed a simple protocol dedicated to this software over http and achieved a speedup of 550 times with 600 CPU cores. With such speed ups, we are able to perform faster high-throughput computations on large number of protein structures.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 169.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 219.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Deng, B., Zhu, S., Macklin, A.M., Xu, J., Lento, C., Sljoka, A., et al.: Suppressing allostery in epitope mapping experiments using millisecond hydrogen/deuterium exchange mass spectrometry. MAbs 9(8), 1327–36 (2017). https://doi.org/10.1080/19420862.2017.1379641

    Article  Google Scholar 

  2. Jacobs, D.J., Rader, A.J., Kuhn, L.A., Thorpe, M.F.: Protein flexibility predictions using graph theory. Proteins 44(2), 150–65 (2001). https://doi.org/10.1002/prot.1081

    Article  Google Scholar 

  3. Jeliazkov, J.R., Sljoka, A., Kuroda, D., Tsuchimura, N., Katoh, N., Tsumoto, K., Gray, J.J.: Repertoire analysis of antibody CDR-H3 loops suggests affinity maturation does not typically result in rigidification. Front. Immunol. 9, 413 (2018). https://doi.org/10.3389/fimmu.2018.00413

    Article  Google Scholar 

  4. Kim, T.H., Mehrabi, P., Ren, Z., Sljoka. A., Ing, C., Bezginov, A., et al.: The role of dimer asymmetry and protomer dynamics in enzyme catalysis. Science 355(6322) (2017). https://doi.org/10.1126/science.aag2355

    Article  Google Scholar 

  5. Sljoka, A.: Algorithms in rigidity theory with applications to protein flexibility and mechanical linkages. Ph.D. thesis, Graduate Programme in Mathematics and Statistics, York University, Toronto, Canada (2012)

    Google Scholar 

  6. Sljoka, A., Wilson, D.: Probing protein ensemble rigidity and hydrogen-deuterium exchange. Phys. Biol. 10(5), 056013 (2013). https://doi.org/10.1088/1478-3975/10/5/056013

    Article  Google Scholar 

  7. Tsuchimura, N.: Computational results for Gaussian moat problem. IEICE Trans. Fundam. E88-A, 1267–1273(2005)

    Article  Google Scholar 

  8. Whiteley. W: Counting out to the fexibility of molecules. Phys. Biol. 2, S116–S126 (2005). https://doi.org/10.1088/1478-3975/2/4/S06

    Article  Google Scholar 

  9. Wildman, H.K., Kern, K.: Dynamic personalities of proteins. Nature 450, 964–972 (2007). https://doi.org/10.1038/nature06522

    Article  Google Scholar 

  10. Woltman, G., Kurowski, S.: GIMPS. https://www.mersenne.org/

  11. The BOINC project: Berkeley Open Infrastructure for Network Computing. http://boinc.berkeley.edu/

  12. The PVM Project Team: PVM. https://www.csm.ornl.gov/pvm/

  13. Software in the Public Interest, Inc.: Open MPI. https://www.open-mpi.org/

  14. University of California Berkeley: SETI@home. http://setiathome.ssl.berkeley.edu/

Download references

Acknowledgements

The authors would like to acknowledge Naoki Katoh for letting us start collaborative research through CREST project. The authors were supported by JST CREST Grant Number JPMJCR1402 (Japan).

Author information

Authors and Affiliations

  1. Department of Informatics, School of Science and Technology, Kwansei Gakuin University, Sanda, Hyogo, Japan

    Nobuyuki Tsuchimura & Adnan Sljoka

Authors
  1. Nobuyuki Tsuchimura
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Adnan Sljoka
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Nobuyuki Tsuchimura .

Editor information

Editors and Affiliations

  1. Universitat Politècnica de Catalunya, Barcelona, Spain

    Fatos Xhafa

  2. Department of Information and Communication Engineering, Faculty of Information Engineering, Fukuoka Institute of Technology, Fukuoka-shi, Fukuoka-ken, Japan

    Leonard Barolli

  3. Faculty of Management, Comenius University in Bratislava, Bratislava, Slovakia

    Michal Greguš

Rights and permissions

Reprints and permissions

Copyright information

© 2019 Springer Nature Switzerland AG

About this paper

Check for updates. Verify currency and authenticity via CrossMark

Cite this paper

Tsuchimura, N., Sljoka, A. (2019). Distributed Computation for Protein Structure Analysis. In: Xhafa, F., Barolli, L., Greguš, M. (eds) Advances in Intelligent Networking and Collaborative Systems. INCoS 2018. Lecture Notes on Data Engineering and Communications Technologies, vol 23. Springer, Cham. https://doi.org/10.1007/978-3-319-98557-2_2

Download citation

Publish with us

Policies and ethics

Search

Navigation