Skip to main content

Volunteer Computing Project SiDock@home for Virtual Drug Screening Against SARS-CoV-2

  • Conference paper
  • First Online:
Computer Science Protecting Human Society Against Epidemics (ANTICOVID 2021)


In this paper, we describe a volunteer computing project SiDock@home aimed at high-throughput virtual screening of a specially developed library of small compounds against a set of targets playing important roles in the life-cycle of the virus. The originality of the screening library and the molecular docking software allows us to obtain new knowledge about chemical space in relation to SARS-CoV-2. At the same time, the existing volunteer computing community provides us with a large computational power. Having risen to a size of a modern supercomputer in several months, SiDock@home becomes an independent general drug discovery project, with its first mission targeting SARS-CoV-2.

Supported by the Scholarship of the President of the Russian Federation for young scientists and graduate students (project SP-609.2021.5), the Slovenian Ministry of Science and Education infrastructure, project grant HPC-RIVR, by the Slovenian Research Agency (ARRS), programme P2-0046 and J1-2471, the Physical Chemistry programme grant P1-0201; Slovenian Ministry of Education, Science and Sports programme grant OP20.04342.

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

Access this chapter

USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
USD 79.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 99.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 99.99
Price excludes VAT (USA)
  • Durable hardcover 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


  1. Anderson, D.P.: BOINC: a platform for volunteer computing. J. Grid Comput. 18(1), 99–122 (2020)

    Article  Google Scholar 

  2. Blanzieri, E., et al.: A computing system for discovering causal relationships among human genes to improve drug repositioning. IEEE Trans. Emerg. Topics Comput. pp. 1–1 (2020).

  3. BOINC combined - Detailed stats – BOINCstats/BAM! Accessed 30 Jun 2021

  4. By Editorial Team: The history of supercomputing vs. COVID-19. Accessed 18 Mar 2021

  5. Cao, L., et al.: De novo design of picomolar SARS-CoV-2 miniprotein inhibitors. Science 370(6515), 426–431 (2020).,

  6. Cloud Computing Services – Microsoft Azure. Accessed 30 Jun 2021

  7. CmDock. Accessed 30 Jun 2021

  8. De Salazar, P.M., Ramos, J., Cruz, V.L., Polo, R., Del Amo, J., Martínez-Salazar, J.: Tenofovir and remdesivir ensemble docking with the SARS-CoV-2 polymerase and template-nascent RNA. Authorea Preprints (2020)

    Google Scholar 

  9. Distributed Computing - Computing Platforms. Accessed 30 Jun 2021

  10. Folding@home - fighting disease with a world wide distributed super computer. Accessed 30 Jun 2021

  11. Home - COVID.SI. Accessed 30 Jun 2021

  12. Home [Exscalate4COV consortium]. Accessed 30 Jun 2021

  13. IberCIVIS. Accessed 30 Jun 2021

  14. Institute for Protein design, University of Washington: Rosetta’s role in fighting coronavirus. Accessed 30 Jun 2021

  15. Ivashko, E., Nikitina, N.: Replication of “tail’’ computations in a desktop grid project. In: Voevodin, V., Sobolev, S. (eds.) RuSCDays 2020. CCIS, vol. 1331, pp. 611–621. Springer, Cham (2020).

    Chapter  Google Scholar 

  16. Jukič, M., Janežič, D., Bren, U.: Ensemble docking coupled to linear interaction energy calculations for identification of coronavirus main protease (3CLpro) non-covalent small-molecule inhibitors. Molecules 25(24), 5808 (2020)

    Article  Google Scholar 

  17. Jukič, M., Škrlj, B., Tomšič, G., Pleško, S., Podlipnik, Č, Bren, U.: Prioritisation of compounds for 3CLpro inhibitor development on SARS-CoV-2 variants. Molecules 26(10), 3003 (2021)

    Article  Google Scholar 

  18. Mandala, V.S., McKay, M.J., Shcherbakov, A.A., Dregni, A.J., Kolocouris, A., Hong, M.: Structure and drug binding of the SARS-CoV-2 envelope protein transmembrane domain in lipid bilayers. Nat. Struct. Mole. Biol. 27(12), 1202–1208 (2020)

    Article  Google Scholar 

  19. Modeling of the SARS-COV-2 Genome using I-TASSER. Accessed 30 Jun 2021

  20. Morley, S.D., Afshar, M.: Validation of an empirical RNA-ligand scoring function for fast flexible docking using RiboDock®. J. Comput.-aided Mole. Des. 18(3), 189–208 (2004)

    Article  Google Scholar 

  21. Multi-step protocol for HTVS – RxDock 0.1.0 documentation. Accessed 30 Jun 2021

  22. Nikitina, N., Manzyuk, M., Podlipnik, C., Jukić, M.: Performance estimation of a BOINC-based Desktop Grid for large-scale molecular docking. In: 16th International Conference on Parallel Computing Technologies,PaCT-2021, submitted, 2021

    Google Scholar 

  23. Ongoing Projects – RIKEN Center for Computational Science RIKEN Website. Accessed 30 Jun 2021

  24. OpenPandemics - COVID-19 – Research – World Community Grid. accessed 30 Jun 2021

  25. Projects – COVID-19 HPC Consortium. Accessed 30 Jun 2021

  26. Puranen, J.S., Vainio, M.J., Johnson, M.S.: Accurate conformation-dependent molecular electrostatic potentials for high-throughput in silico drug discovery. J. Comput. Chem. 31(8), 1722–1732 (2010)

    Google Scholar 

  27. Ruiz-Carmona, S., et al.: rDock: a fast, versatile and open source program for docking ligands to proteins and nucleic acids. PLoS Comput. Biol. 10(4), e1003571 (2014)

    Google Scholar 

  28. Science United. Accessed 30 Jun 2021

  29. Science United and COVID-19. 30 Jun 2021

  30. Shin, D., et al.: Papain-like protease regulates SARS-CoV-2 viral spread and innate immunity. Nature 587(7835), 657–662 (2020)

    Article  Google Scholar 

  31. Shoichet, B.K., McGovern, S.L., Wei, B., Irwin, J.J.: Lead discovery using molecular docking. Curr. Opin. Chem. Biol. 6(4), 439–446 (2002)

    Article  Google Scholar 

  32. SiDock@home. Accessed 30 Jun 2021

  33. TN-Grid. Accessed 30 Jun 2021

  34. UTEP school of pharmacy developing COVID-19 vaccine, drug treatments using supercomputing.,-drug-treatments-using-supercomputing.html (2021). Accessed 30 Jun 2021

  35. Vainio, M.J., Johnson, M.S.: Generating conformer ensembles using a multiobjective genetic algorithm. J. Chem. Inf. Model. 47(6), 2462–2474 (2007)

    Article  Google Scholar 

  36. World Community Grid - home. Accessed 30 Jun 2021

  37. Wrapp, D., et al.: Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation. Science 367(6483), 1260–1263 (2020)

    Article  Google Scholar 

  38. WrapperApp - BOINC. Accessed 30 Jun 2021

Download references


The first initial library (one billion of compounds) was prepared with the generous help of Microsoft that donated computational resources in the Azure cloud platform [6]. We all from COVID.SI are grateful and looking forward to future collaborations.

We wholeheartedly thank all BOINC participants for their contributions.

Author information

Authors and Affiliations


Corresponding author

Correspondence to Natalia Nikitina .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2021 IFIP International Federation for Information Processing

About this paper

Check for updates. Verify currency and authenticity via CrossMark

Cite this paper

Nikitina, N., Manzyuk, M., Podlipnik, Č., Jukić, M. (2021). Volunteer Computing Project SiDock@home for Virtual Drug Screening Against SARS-CoV-2. In: Byrski, A., Czachórski, T., Gelenbe, E., Grochla, K., Murayama, Y. (eds) Computer Science Protecting Human Society Against Epidemics. ANTICOVID 2021. IFIP Advances in Information and Communication Technology, vol 616. Springer, Cham.

Download citation

  • DOI:

  • Published:

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-030-86581-8

  • Online ISBN: 978-3-030-86582-5

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics