Grid enabled virtual screening against malaria

• Main Authors: Jacq, N., Salzemann, J., Jacq, F., Legre, Yannick, Medernach, E., Montagnat, Johan, Maass, A., Reichstadt, Matthieu, Schwichtenberg, H., Sridhar, M., Kasam, V., Zimmermann, M., Hofmann, M., Breton, Vincent
• Other Authors: Laboratoire de Physique Corpusculaire - Clermont-Ferrand (LPC), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Communication & Systèmes Toulouse (C-S), Communication & Systèmes-CS-SI France, Laboratoire d'Informatique, Signaux, et Systèmes de Sophia Antipolis (I3S), Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), Fraunhofer Institute for Algorithms and Scientific Computing (Fraunhofer SCAI), Fraunhofer (Fraunhofer-Gesellschaft)
• Format: Article in Journal/Newspaper
• Language: English
• Published: HAL CCSD 2008
• Subjects: Data challenge; drug discovery; grid computing; grid infrastructure; in silico docking; virtual screening; malaria; [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM]; [INFO.INFO-DC]Computer Science [cs]/Distributed; Parallel; and Cluster Computing [cs.DC]; Avian flu
• Online Access: https://hal.in2p3.fr/in2p3-00114120; https://hal.in2p3.fr/in2p3-00114120/document; https://hal.in2p3.fr/in2p3-00114120/file/Jour_Grid_Comp_.pdf

34 pages, 5 figures, 3 tables, to appear in Journal of Grid Computing - PCSV, à paraître dans Journal of Grid Computing WISDOM is an international initiative to enable a virtual screening pipeline on a grid infrastructure. Its first attempt was to deploy large scale in silico docking on a public grid infrastructure. Protein-ligand docking is about computing the binding energy of a protein target to a library of potential drugs using a scoring algorithm. Previous deployments were either limited to one cluster, to grids of clusters in the tightly protected environment of a pharmaceutical laboratory or to pervasive grids. The first large scale docking experiment ran on the EGEE grid production service from 11 July 2005 to 19 August 2005 against targets relevant to research on malaria and saw over 41 million compounds docked for the equivalent of 80 years of CPU time. Up to 1,700 computers were simultaneously used in 15 countries around the world. Issues related to the deployment and the monitoring of the in silico docking experiment as well as experience with grid operation and services are reported in the paper. The main problem encountered for such a large scale deployment was the grid infrastructure stability. Although the overall success rate was above 80%, a lot of monitoring and supervision was still required at the application level to resubmit the jobs that failed. But the experiment demonstrated how grid infrastructures have a tremendous capacity to mobilize very large CPU resources for well targeted goals during a significant period of time. This success leads to a second computing challenge targeting Avian Flu neuraminidase N1.