High-performance virtual screening in a BOINC-based enterprise desktop grid

Authors

  • Evgeny E. Ivashko Институт прикладных математических исследований Карельского научного центра РАН
  • Nataly N. Nikitina Институт прикладных математических исследований Карельского научного центра РАН
  • Steffen Moeller University of Lübeck, The Lübeck Institute of Experimental Dermatology

DOI:

https://doi.org/10.14529/cmse150105

Keywords:

desktop grid, enterprise desktop grid, distributed computing, virtual screening

Abstract

In the paper we present the experience of developing and using an Enterprise Desktop Grid infrastructure based on BOINC software platform and designed for virtual screening using open-source software and open databases of chemical compounds models. According to the idea of Enterprise Desktop Grid, a virtual single computational network integrates non-specialized computers within an organization or group of users that are directly interested in solving an applied problem. We describe and evaluate the performance of the infrastructure created withing a joint research project between the L¨ubeck Institute of Experimental Dermatology (former Clinic of dermatology, allergology and venerology) of the University of L¨ubeck and the Institute of Applied Mathematical Research of the Karelian Research Centre of the Russian Academy of Sciences. We summarize the project and briefly overview the results of the virtual screening.

References

Ивашко, Е.Е. Desktop Grid корпоративного уровня / Е.Е. Ивашко — Программные системы: теория и приложения. — 2014. — №1(19). — С. 183–190.

Anderson, D.P. BOINC: A system for public-resource computing and storage / D.P. Anderson // R. Buyya (Editor), Fifth IEEE/ACM International Workshop on Grid Computing. — 2004. — P. 4–10.

Breakthrough in the fight against childhood cancer. URL: http://www.worldcommunitygrid.org/about_us/viewNewsArticle.do?articleId=342 (дата обращения: 14.11.2014).

ChemSpider: Search and share chemistry. URL: http://www.chemspider.com (дата обращения: 14.11.2014).

Del Rio, A. CoCoCo: a free suite of multiconformational chemical databases for high-throughput virtual screening purposes / A. Del Rio, A.J. Moura Barbosa, F. Caporuscio, G.F. Mangiatordi — Molecular BioSystems. — 2010. — No. 6. — P. 2122–2128.

Irwin, J.J. ZINC: A Free Tool to Discover Chemistry for Biology / J.J. Irwin, T. Sterling, M.M. Mysinger, et al. — Journal of Chemical Information and Modeling. — 2012. — No. 52(7). — P. 1757–1768.

Matter, H. Applications and Success Stories in Virtual Screening / H. Matter, C. Sotriffer — Virtual Screening: Principles, Challenges, and Practical Guidelines (ed. C. Sotriffer). Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim, Germany, 2011. — P. 319–358.

Moura Barbosa, A.J. Freely accessible databases of commercial compounds for high-throughput virtual screenings / A.J. Moura Barbosa, A. Del Rio — Current Topics in Medicinal Chemistry. — 2012. — No. 12. — P. 866–877.

Trott, O. AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization and multithreading / O. Trott, A.J. Olson — Journal of Computational Chemistry. — 2010. — No. 31. — P. 455–461.

Villoutreix, B.O. Structure-based virtual ligand screening: recent success stories / B.O. Villoutreix, R. Eudes, M.A. Miteva — Combinatorial chemistry & high throughput screening. — 2009. — No. 12(10). — P. 1000–1016.

Walters, W.P. Virtual screening an overview / W.P. Walters, M.T. Stahl, M.A. Murcko — Drug Discovery Today. — 1998. — Vol. 3, No. 4. — P. 160–178.

Published

2014-12-22

Issue

Section

Informatics, Computers and Control