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2-15 November 2008.

META-DOCK Final Report. Jérôme Verleyen Juan Manuel Hurtado Rámirez Enrique M e rino Pérez. 2-15 November 2008. Recall docking…. Database of 5000 Ligands. Receptor. The problem here is do it faster. The ways to execute this process. One Search ~ 20 minutes.

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2-15 November 2008.

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  1. META-DOCK Final Report Jérôme Verleyen Juan Manuel Hurtado Rámirez Enrique Merino Pérez 2-15 November 2008.

  2. Recall docking… Database of 5000 Ligands Receptor The problem here is do it faster

  3. The ways to execute this process One Search ~ 20 minutes 5000 Searchs ~ 100 000 minutes Desktop-PC ~70 days Cluster (100 nodes) 16 Hrs GRID ?

  4. Solution designed in EELA Grid School Binary, Ligands LFC WN SE WN WMS CE WN WN User interfase AMGA INPUT FILES 4

  5. JDL SUMARIZE JDL COLLECTION LFC SHELL SCRIPT LIGANDS SCRIPT PERL CONF conf_SE_HOST="m09-e2gris1.eela.ufrj.br" conf_LFC_DIR="/grid/e2gris1.vo.eu-eela.eu/mexico/MetaDock" conf_LCG_CATALOG_TYPE=lfc conf_LFC_HOST=m02-e2gris1.eela.ufrj.br …

  6. -Init of the job -DPF file calculation -Autogrid calculation -Autodock calculation -Upload to SE of dlg file -End of the job JDL SUMARIZE JDL COLLECTION AMGA Binary, Ligands WN MONITOR SCRIPT SUMMARIZE SCRIPT SHELL SCRIPT SE Results 6

  7. [app11@m111-e2gris1 WhyErrorAutogrid]$ test_monitor.pl • Reading file : /home/app11/WhyErrorAutogrid/COL.ID • colId :fb4eIbwNgfG954kfyQpM • -- • Global status of process: Running • _____________________________________ • Status of each process in WMS • Individual status Done : 0 • Individual status Scheduled : 34 • Individual status Running : 6 • Individual status Aborted : 0 • Total jobs sends : 40 • _____________________________________ • Status of of jobs in WN • Init of the job : 1 2.50 % • Autogrid calculation : 0 0.00 % • DPF file calculation : 4 10.00 % • Autodock calculation : 0 0.00 % • Upload to SE of dlg file : 0 0.00 % • End of the job : 0 0.00% • Total : 5 12.50%

  8. [app11@m111-e2gris1 WhyErrorAutogrid]$ test_monitor.pl -v • Reading file : /home/app11/WhyErrorAutogrid/COL.ID • colId :fb4eIbwNgfG954kfyQpM • Global status : Running • colId state ligandName reason date • 0 20apEL4OUhjH_ciiXZVlwA fb4eIbwNgfG954kfyQpM 1 ZINC00008492 autogrid calculation 1226692243 • 1 iNY6yfA6aew9UPNVoeyDKQ fb4eIbwNgfG954kfyQpM 1 ZINC00001863 autogrid calculation 1226692244 • 2 OeBQBqYmNDJfCodHZigNLw fb4eIbwNgfG954kfyQpM 1 ZINC00001883 autogrid calculation 1226692252 • 3 FJPE8i-nNTqYW48LkFEesA fb4eIbwNgfG954kfyQpM 1 ZINC00032351 autogrid calculation 1226692278

  9. Some results:

  10. PERSPECTIVES: • - Add Web interface. • - OrganizingLigandsusingamga (characteristics). • - Add more databases. • - Implementanautomatic control system.

  11. Acknowledgementto: • EELA Organization. • All INSTRUCTORS!! • Allmanagementsupport. • Allpartners. • ALL. • MUITO OBRIGADO!!!

  12. ?

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