dorsal/arxiv
View SchemaGrid enabled virtual screening against malaria
| Authors | N. Jacq, J. Salzemann, F. Jacq, Y. Legré, E. Medernach, J. Montagnat, A. Maass, M. Reichstadt, H. Schwichtenberg, M. Sridhar, V. Kasam, M. Zimmermann, M. Hofmann, V. Breton |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0611054 |
| URL | https://arxiv.org/abs/q-bio/0611054 |
| Journal | Journal of Grid Computing 6 (2008) 29-43 |
Abstract
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.
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"abstract": "WISDOM is an international initiative to enable a virtual screening pipeline\non a grid infrastructure. Its first attempt was to deploy large scale in silico\ndocking on a public grid infrastructure. Protein-ligand docking is about\ncomputing the binding energy of a protein target to a library of potential\ndrugs using a scoring algorithm. Previous deployments were either limited to\none cluster, to grids of clusters in the tightly protected environment of a\npharmaceutical laboratory or to pervasive grids. The first large scale docking\nexperiment ran on the EGEE grid production service from 11 July 2005 to 19\nAugust 2005 against targets relevant to research on malaria and saw over 41\nmillion compounds docked for the equivalent of 80 years of CPU time. Up to\n1,700 computers were simultaneously used in 15 countries around the world.\nIssues related to the deployment and the monitoring of the in silico docking\nexperiment as well as experience with grid operation and services are reported\nin the paper. The main problem encountered for such a large scale deployment\nwas the grid infrastructure stability. Although the overall success rate was\nabove 80%, a lot of monitoring and supervision was still required at the\napplication level to resubmit the jobs that failed. But the experiment\ndemonstrated how grid infrastructures have a tremendous capacity to mobilize\nvery large CPU resources for well targeted goals during a significant period of\ntime. This success leads to a second computing challenge targeting Avian Flu\nneuraminidase N1.",
"arxiv_id": "q-bio/0611054",
"authors": [
"N. Jacq",
"J. Salzemann",
"F. Jacq",
"Y. Legr\u00e9",
"E. Medernach",
"J. Montagnat",
"A. Maass",
"M. Reichstadt",
"H. Schwichtenberg",
"M. Sridhar",
"V. Kasam",
"M. Zimmermann",
"M. Hofmann",
"V. Breton"
],
"categories": [
"q-bio.QM",
"cs.DC"
],
"journal_ref": "Journal of Grid Computing 6 (2008) 29-43",
"title": "Grid enabled virtual screening against malaria",
"url": "https://arxiv.org/abs/q-bio/0611054"
},
"schema_id": "dorsal/arxiv",
"source": {
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