Skip to main content
SpringerLink
Log in

New Smart Optimal Transition Molecules Structure Approach from Discrete to Continuous Based on Three-Dimensional Analysis Method

  • Conference paper
  • First Online:
International Conference on Advanced Intelligent Systems for Sustainable Development (AI2SD’2023) (AI2SD 2023)

Part of the book series: Lecture Notes in Networks and Systems ((LNNS,volume 905))

  • 43 Accesses

Abstract

To understand the relationship between a molecule’s function and its three-dimensional structure, researchers have been studying the evolution and mutations of the SARS-CoV-2 virus. This research focuses on identifying interaction areas between the viral spike and human cell receptors for developing treatments. In this work, a novel approach based on shape alignment and residue interaction region identification is proposed. Experimental studies using dynamic programming and Cubic Spline polynomial interpolation show promising results, making the approach highly effective.

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

Similar content being viewed by others

References

  1. Jindal, S., Sharma, A., Joshi, A., Gupta, M.: Artificial intelligence fuelling the health care. In: Marriwala, N., Tripathi, C.C., Kumar, D., Jain, S. (eds) Mobile Radio Communications and 5G Networks. Lecture Notes in Networks and Systems, vol. 140, pp. 501–507 . Springer, Singapore (2021). https://doi.org/10.1007/978-981-15-7130-5_40

  2. Salman, M., Ahmed, A.W., Khan, O.A., Raza, B., Latif, K.: Artificial intelligence in bio-medical domain an overview of AI based innovations in medical. Int. J. Adv. Comput. Sci. Appl. (IJACSA), 8(8) (2017). https://doi.org/10.14569/IJACSA.2017.080842

  3. Chokri, S., Daoud, W.B., Hanini, W., Mahfoudhi, S., Makhlouf, A.: AI-based system for the detection and prevention of COVID-19. Int. J. Adv. Comput. Sci. Appl. (IJACSA) 13(1) (2022). https://doi.org/10.14569/IJACSA.2022.0130171

  4. Verma, S., Gazara, R.K.: Big data analytics for understanding and fighting COVID-19. In: Raza, K. (eds.) Computational Intelligence Methods in COVID-19: Surveillance, Prevention, Prediction and Diagnosis. Studies in Computational Intelligence, vol. 923. Springer, Singapore, pp. 333–348 (2021). https://doi.org/10.1007/978-981-15-8534-0_17

  5. World Health Organization, Tracking SARS-CoV-2 variants. https://www.who.int/health-topics/nipah-virus-infection/tracking-SARS-CoV-2-variants. Accessed 05 Jun 2022

  6. McLean. G., et al.: The impact of evolving SARS-CoV-2 mutations and variants on COVID-19 vaccines. mBio 13(2), e02979–21 (2022). https://doi.org/10.1128/mbio.02979-21

  7. Rahardi, M., Aminuddin, A., Fauzi Abdulloh, F., Adhi Nugroho, R.: Sentiment analysis of Covid-19 vaccination using support vector machine in Indonesia. Int. J. Adv. Comput. Sci. Appl. (IJACSA) 13(6) (2022). https://doi.org/10.14569/IJACSA.2022.0130665

  8. Ou, J., et al.: Tracking SARS-CoV-2 Omicron diverse spike gene mutations identifies multiple inter-variant recombination events. Signal Transduct. Target. Ther. 7(1), 138 (2022). https://doi.org/10.1038/s41392-022-00992-2

    Article  Google Scholar 

  9. Rhalem, W., et al.: An efficient and rapid method for detection of mutations in deoxyribonucleic acid – sequences. In: International Journal of Advanced Computer Science and Applications (IJACSA), vol. 11, no. 4 (2020). https://doi.org/10.14569/IJACSA.2020.0110438

  10. RCSB Protein Data Bank, RCSB PDB: Homepage. https://www.rcsb.org/. Accessed 06 Jun 2022

  11. Holm, L., Rosenström, P.: Dali server: conservation mapping in 3D. Nucleic Acids Res. 38, no. Web Server issue, W545–549 (2010). https://doi.org/10.1093/nar/gkq366

  12. Shindyalov, I.N., Bourne, P.E.: Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Eng. Des. Sel. 11(9), 739–747 (1998). https://doi.org/10.1093/protein/11.9.739

    Article  Google Scholar 

  13. Wiederstein, M., Sippl, M.J.: TopMatch-web: pairwise matching of large assemblies of protein and nucleic acid chains in 3D. Nucleic Acids Res. 48(W1), W31–W35 (2020). https://doi.org/10.1093/nar/gkaa366

    Article  Google Scholar 

  14. Maiti, R., Van Domselaar, G.H., Zhang, H., Wishart, D.S.: SuperPose: a simple server for sophisticated structural superposition. Nucleic Acids Res. 32, no. Web Server, W590–W594 (2004). https://doi.org/10.1093/nar/gkh477

  15. Needleman, S.B., Wunsch, C.D.: A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol. 48(3), 443–453 (1970). https://doi.org/10.1016/0022-2836(70)90057-4

    Article  Google Scholar 

  16. NCSTR of Morocco, The high performance computing platform (HPC) (2022). https://hpc.marwan.ma/. Accessed 06 Jun 2022

  17. Jmol: an open-source Java viewer for chemical structures in 3D. http://jmol.sourceforge.net/

  18. Li, F., Li, W., Farzan, M., Harrison, S.C.: Structure of SARS coronavirus spike receptor-binding domain complexed with receptor. Science 309(5742), 1864–1868 (2005). https://doi.org/10.1126/science.1116480

    Article  Google Scholar 

  19. Wu, K., Li, W., Peng, G., Li, F.: Crystal structure of NL63 respiratory coronavirus receptor-binding domain complexed with its human receptor. Proc. Natl. Acad. Sci. 106(47), 19970–19974 (2009). https://doi.org/10.1073/pnas.0908837106

    Article  Google Scholar 

  20. Maiti, R., et al.: SuperPose: a simple server for sophisticated structural superposition. Nucleic Acids Res. 32, W590–W594 (2004). https://doi.org/10.1093/nar/gkh477

  21. Wiederstein, M., Sippl, M.J.: TopMatch-web: pairwise matching of large assemblies of protein and nucleic acid chains in 3D. Nucleic Acids Res. 48, W31–W35 (2020). https://doi.org/10.1093/nar/gkaa366

    Article  Google Scholar 

Download references

Acknowledgment

This work was supported by the “Urgence COVID-19” fundraising campaign of the Institut Pasteur. The National Center for Scientific and Technical Research (CNRST) in Rabat also supported this research by providing computational resources of HPC-MARWAN (hpc.marwan.ma).

Author information

Authors and Affiliations

  1. E2SN Research Team, ENSAM, Mohammed V University in Rabat, Rabat, Morocco

    Wajih Rhalem, Sory Millimono, Larbi Bellarbi & Nabil Aqili

  2. Moroccan Society of Digital Health, Rabat, Morocco

    Wajih Rhalem, Sory Millimono & Nassim Kharmoum

  3. Department of Surgery, School of Medicine, Mohammed VI University of Health Sciences, Casablanca, Morocco

    Lahcen Belyamani

  4. Environmental Health Laboratory, Department of Research, Pasteur Institute, Casablanca, Morocco

    Salsabil Hamdi

  5. National Center for Scientific and Technical Research Rabat, Rabat, Morocco

    Nassim Kharmoum & Hassan Ghazal

  6. Emergency Department, Mohammed the Vth Military Training Hospital, Mohammed V University in Rabat, Rabat, Morocco

    Said Jidane

  7. Computer Sciences Department, Faculty of Sciences and Techniques of Tangier, University of Abdelmalek Essaadi, Tangier, Morocco

    Mostafa Ezziyani

  8. Mohammed VI Center for Research and Innovation, Rabat, Morocco

    Wajih Rhalem, Sory Millimono, Larbi Bellarbi, Nabil Aqili, Najib Alidrissi, Salsabil Hamdi, Nassim Kharmoum, Asma Chaik Said, Said Jidane, Lahcen Belyamani, Hassan Ghazal & Mostafa Ezziyani

  9. Laboratory of Genomics, Bioinformatics and Digital Health, Mohammed VI University of Sciences and Health, Casablanca, Morocco

    Najib Alidrissi

  10. Research Team in Biomedical Engineering and Pharmaceutical Sciences, ENSAM, Mohammed V University in Rabat, Rabat, Morocco

    Asma Chaik Said

Authors
  1. Wajih Rhalem
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Sory Millimono
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Larbi Bellarbi
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Nabil Aqili
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Najib Alidrissi
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Salsabil Hamdi
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Nassim Kharmoum
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Asma Chaik Said
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Said Jidane
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Lahcen Belyamani
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. Hassan Ghazal
    View author publications

    You can also search for this author in PubMed Google Scholar

  12. Mostafa Ezziyani
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Wajih Rhalem .

Editor information

Editors and Affiliations

  1. Computer Sciences Department, Faculty of Sciences and Techniques of Tangier, Abdelmalek Essaâdi University, Tangier, Morocco

    Mostafa Ezziyyani

  2. Systems Research Institute, Polish Academy of Science, Warsaw, Poland

    Janusz Kacprzyk

  3. Department of Automatics and Applied Software at the Faculty of Engineering, University "Aurel Vlaicu" Arad and Romanian Academy of Scientists, Arad, Romania

    Valentina Emilia Balas

Rights and permissions

Reprints and permissions

Copyright information

© 2024 The Author(s), under exclusive license to Springer Nature Switzerland AG

About this paper

Check for updates. Verify currency and authenticity via CrossMark

Cite this paper

Rhalem, W. et al. (2024). New Smart Optimal Transition Molecules Structure Approach from Discrete to Continuous Based on Three-Dimensional Analysis Method. In: Ezziyyani, M., Kacprzyk, J., Balas, V.E. (eds) International Conference on Advanced Intelligent Systems for Sustainable Development (AI2SD’2023). AI2SD 2023. Lecture Notes in Networks and Systems, vol 905. Springer, Cham. https://doi.org/10.1007/978-3-031-52385-4_29

Download citation

Publish with us

Policies and ethics

Search

Navigation