Abstract
Large scale grids for in silico drug discovery open opportunities of particular interest to neglected and emerging diseases. In 2005 and 2006, we have been able to deploy large scale virtual docking within the framework of the WISDOM initiative against malaria and avian influenza requiring about 100 years of CPU on the EGEE, Auvergrid and TWGrid infrastructures. These achievements demonstrated the relevance of large scale grids for the virtual screening by molecular docking. This also allowed evaluating the performances of the grid infrastructures and to identify specific issues raised by large scale deployment.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
BCG Estimate: A Revolution in R&D, The Impact of Genomics (2001)
Lyne, P.D.: Structure-based virtual screening: An overview. Drug Discov. Today 7, 1047–1055 (2002)
Congreve, M. et al.: Structural biology and drug discovery. Drug Discov Today 10, 895–907 (2005)
Nwaka, S., Ridley, R.G.: Virtual drug discovery and development for neglected diseases through public-private partnerships. Nat. Rev. Drug Discov 2, 919–928 (2003)
Chien, A. et al.: Grid technologies empowering drug discovery. Drug Discovery Today 7, 176–180 (2002)
Gagliardi, F. et al.: Building an infrastructure for scientific Grid computing: status and goals of the EGEE project. Philosophical Transactions: Mathematical, Physical and Engineering Sciences 363, 1729–1742 and http://www.eu-egee.org/ (2005)
Ghosh, S.: Structure-based virtual screening of chemical libraries for drug discovery. Curr. Opin. Chem. Biol. 10, 194–202 (2006)
Coombs, G.H. et al.: Aspartic proteases of plasmodium falciparum and other protozoa as drug targets. Trends parasitol. 17, 532–537 (2001)
Weisner, J. et al.: Angew. New. Antimalarial drugs, Chem. Int. 42, 5274–5529 (2003)
Curtis, C.F., Hoffman, S.L.: Science 290, pp. 1508–1509 (2000)
Spencer, R.W.: Highthroughput virtual screening of historic collections on the file size, biological targets, and file diversity. Biotechnol. Bioeng 61, 61–67 (1998)
Jacq, N.: Grid as a bioinformatics tool. Parallel Computing 30, 1093–1107 (2004)
Campana, S. et al.: Analysis of the ATLAS Rome Production Experience on the LHC Computing Grid. IEEE International Conference on e-Science and Grid Computing (2005)
Bird, I. et al.: Operating the LCG and EGEE production Grids for HEP. Proceedings of the CHEP’04 Conference (2004)
Breton, V. et al.: Grid added value to address malaria. In: Proceedings of the 6-th IEEE International Symposium on Cluster Computing and the Grid 40, http://wisdom. healthgrid.org/ (2006)
Altschul, S.F. et al.: Basic local alignment search tool. J. Mol. Biol. 215, 403–410 (1990)
Ziegler, R.: Pharma GRIDs: Key to Pharmaceutical Innovation? In: Proceedings of the HealthGrid conference 2004 (2004)
Jacq, N. et al.: Demonstration of In Silico Docking at a Large Scale on Grid Infrastructure. Studies in Health Technology and Informatics 120, 155–157 (2006)
Francis, S.E. et al.: Hemoglobin metabolism in the malaria parasite plasmodium falciparum. Annu.Rev. Microbiol. 51, 97–123 (1997)
Lee, H.-C. et al.: Grid-enabled High-throughput in silico Screening against influenza A Neuraminidase. To be published in IEEE Transaction on Nanobioscience (2006)
Moscicki, J.T.: DIANE - Distributed Analysis Environment for GRID-enabled Simulation and Analysis of Physics Data. NSS IEEE 2004 (2004)
Moscicki, J.T. et al.: Biomedical Applications on the GRID: Efficient Management of Parallel Jobs. NSS IEEE 2003 (2003)
Li, K.S. et al.: Genesis of a highly pathogenic and potentially pandemic H5N1 influenza virus in eastern Asia. Nature 430, 209–213 (2004)
de Jong, M.D. et al.: Oseltamivir Resistance during Treatment of Influenza A (H5N1) Infection. N. Engl. J. Med. 353, 2667–2672 (2005)
Morris, G.M. et al.: Automated Docking Using a Lamarckian Genetic Algorithm and Empirical Binding Free Energy Function. J. Computational Chemistry 19, 1639–1662 (1998)
Gropp, W., Lusk, E.: Dynamic process management in an MPI setting. In: Proceedings of the 7th IEEE Symposium on Parallel and Distributed Processing (1995)
Rarey, M. et al.: A fast flexible docking method using an incremental construction algorithm. J. Mol. Biol. 261, 470–489 (1996)
Silva, A.M. et al.: Structure and inhibition of plasmepsin II, A haemoglobin degrading enzyme from Plasmodium falciparum. Proc. Natl. Acad. Sci. USA 93, 10034–10039 (1996)
Lamb, M.L., Jorgensen, W.L.: Computational approaches to molecular recognition. Curr. Opin. Chem. Biol. 1, 449 (1997)
Case, D.A. et al.: The Amber biomolecular simulation programs. J. Computat. Chem. 26, 1668–1688 (2005)
Author information
Authors and Affiliations
Editor information
Rights and permissions
Copyright information
© 2007 Springer Berlin Heidelberg
About this paper
Cite this paper
Jacq, N. et al. (2007). Grid-Enabled High Throughput Virtual Screening. In: Dubitzky, W., Schuster, A., Sloot, P.M.A., Schroeder, M., Romberg, M. (eds) Distributed, High-Performance and Grid Computing in Computational Biology. GCCB 2007. Lecture Notes in Computer Science(), vol 4360. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-69968-2_5
Download citation
DOI: https://doi.org/10.1007/978-3-540-69968-2_5
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-69841-8
Online ISBN: 978-3-540-69968-2
eBook Packages: Computer ScienceComputer Science (R0)