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Large Scale In Silico Screening on Grid Infrastructures [article]

N. Jacq, H.-Y. Chen, L.-Y. Ho, M. Hofmann, H.-C. Lee, Y. Legré, S.-C. Lin, A. Maass, E. Medernach, I. Merelli, L. Milanesi, G. Rastelli (+5 others)
2006 arXiv   pre-print
These achievements demonstrated the relevance of large-scale grid infrastructures for the virtual screening by molecular docking.  ...  Large-scale grid infrastructures for in silico drug discovery open opportunities of particular interest to neglected and emerging diseases.  ...  The authors express particular thanks to the site managers in EGEE, TWGrid, AuverGrid for operational supports, the LCG ARDA group for the technical support of DIANE, and the Biomedical Task Force for  ... 
arXiv:cs/0611084v1 fatcat:r6somcqeqbgzrbfdykmqsvzwju

Virtual screening on large scale grids

Nicolas Jacq, Vincent Breton, Hsin-Yen Chen, Li-Yung Ho, Martin Hofmann, Vinod Kasam, Hurng-Chun Lee, Yannick Legré, Simon C. Lin, Astrid Maaß, Emmanuel Medernach, Ivan Merelli (+7 others)
2007 Parallel Computing  
Large scale grids for in silico drug discovery open opportunities of particular interest to neglected and emerging diseases.  ...  These achievements demonstrated the relevance of large scale grids for the virtual screening by molecular docking.  ...  This work was supported in part by Auvergrid, EGEE and TWGrid projects. This work took place in collaboration with the Embrace network of excellence and the BioinfoGRID project.  ... 
doi:10.1016/j.parco.2007.02.010 fatcat:4zghjxovejesfdwl25gdirpoie

Grid-enabled Virtual Screening Against Malaria

N. Jacq, J. Salzemann, F. Jacq, Y. Legré, E. Medernach, J. Montagnat, A. Maaß, M. Reichstadt, H. Schwichtenberg, M. Sridhar, V. Kasam, M. Zimmermann (+2 others)
2007 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.  ...  The main problem encountered for such a large scale deployment was the grid infrastructure stability.  ...  Compared to these initiatives, WISDOM is the first attempt to deploy large scale in silico docking on a public grid infrastructure.  ... 
doi:10.1007/s10723-007-9085-5 fatcat:ebxn7dfkxve6pgeo7tv4mptkie

WISDOM-II: Screening against multiple targets implicated in malaria using computational grid infrastructures

Vinod Kasam, Jean Salzemann, Marli Botha, Ana Dacosta, Gianluca Degliesposti, Raul Isea, Doman Kim, Astrid Maass, Colin Kenyon, Giulio Rastelli, Martin Hofmann-Apitius, Vincent Breton
2009 Malaria Journal  
Results: On the computational side, a sustained infrastructure has been developed: docking at large scale, using different strategies in result analysis, storing of the results on the fly into MySQL databases  ...  In 2005, a first attempt at using grids for large-scale virtual screening focused on plasmepsins and ended up in the identification of previously unknown scaffolds, which were confirmed in vitro to be  ...  (EUMedGrid) who supported the deployment on several grid infrastructures.  ... 
doi:10.1186/1475-2875-8-88 pmid:19409081 pmcid:PMC2691744 fatcat:dbqivtpnojcfzas67rjvuhll6u

Distributed Computing in a Pandemic: A Review of Technologies Available for Tackling COVID-19 [article]

Jamie J Alnasir
2021 arXiv   pre-print
In this article, I review distributed architectures -- various types of clusters, grids and clouds -- that can be leveraged to perform these tasks at scale, at high-throughput, with a high degree of parallelism  ...  Extremely large-scale COVID-19 research has also utilised some of the world's fastest supercomputers, such as IBM's SUMMIT -- for ensemble docking high-throughput screening against SARS-CoV-2 targets for  ...  They have demonstrated this works efficiently at a very large-scale -15K CPUs -with an overhead of only 3.94%.  ... 
arXiv:2010.04700v3 fatcat:kxakuqjlyjfilbroj5nl55xgbq

Large Scale Deployment of Molecular Docking Application on Computational Grid infrastructures for Combating Malaria

Vinod Kasam, Jean Salzemann, Nicolas Jacq, Astrid Mass, Vincent Breton
2007 Seventh IEEE International Symposium on Cluster Computing and the Grid (CCGrid '07)  
The WISDOM project successfully deployed virtual screening at large scale on EGEE grid infrastructures in the summer 2005 and achieved 46 million dockings in 45 days, which is equivalent to 80 CPU years  ...  WISDOM is one good example of a successful deployment of an embarrassingly parallel application. In this paper, we describe the improvements in our deployment.  ...  Information on WISDOM  ... 
doi:10.1109/ccgrid.2007.66 dblp:conf/ccgrid/KasamSJMB07 fatcat:qy2u76mvl5dgbbbppiyfpvhyxi

Wisdom [chapter]

Vincent Breton, Doman Kim, Giulio Rastelli
2009 Grid Computing  
AuverGrid is a project funded by the Conseil Regional d'Auvergne.  ...  The work described in this chapter was partly supported by grants from the European Commission (BioinfoGRID, EGEE, Embrace), the French Miinistry of Research (AGIR, GWENDIA) and the regional authorities  ...  At the end of the large-scale docking deployment, the best 1000 compounds based on scoring were selected thanks to postprocessing ranking jobs deployed on the grid. They were inspected individually.  ... 
doi:10.1201/9781420067682-c14 fatcat:ugdxhna5pnhq7fz7ymtxdw7giq

Grid-Added Value to Address Malaria

V. Breton, N. Jacq, V. Kasam, M. Hofmann-Apitius
2008 IEEE Transactions on Information Technology in Biomedicine  
The first step towards this vision has been achieved during the summer on the EGEE grid infrastructure where 46 million ligands were docked for a total amount of 80 CPU years in 6 weeks in the quest for  ...  Through this paper, we call for a distributed, internet-based collaboration to address one of the worst plagues of our present world, malaria.  ...  EGEE is a project funded by the European Union under contract INFSO-RI-508833. References  ... 
doi:10.1109/titb.2007.895930 pmid:18348947 fatcat:exmzry5gtrd55hmwbiuvcey4ye

Grid Added Value to Address Malaria

V. Breton, N. Jacq, M. Hofmann
2006 Sixth IEEE International Symposium on Cluster Computing and the Grid (CCGRID'06)  
The first step towards this vision has been achieved during the summer on the EGEE grid infrastructure where 46 million ligands were docked for a total amount of 80 CPU years in 6 weeks in the quest for  ...  Through this paper, we call for a distributed, internet-based collaboration to address one of the worst plagues of our present world, malaria.  ...  EGEE is a project funded by the European Union under contract INFSO-RI-508833. References  ... 
doi:10.1109/ccgrid.2006.1630933 fatcat:qk2345didzexzepqoyhlr7eowy

Innovative In Silico Approaches to Address Avian Flu Using Grid Technology

Vincent Breton, Ana da Costa, Paul de Vlieger, Young-Min Kim, Lydia Maigne, Romain Reuillon, David Sarramia, Nam Truong, Hong Nguyen, Doman Kim, Yin-Ta Wu
2009 Infectious Diseases - Drug Targets  
on international grid infrastructures.  ...  For 3 years now, a collaboration of teams in Europe and Asia has been exploring some innovative in silico approaches to better tackle avian flu taking advantage of the very large computing resources available  ...  CURRENT USES OF GRID TECHNOLOGY FOR DRUG DISCOVERY ON AVIAN FLU In silico virtual screening In 2005, the WISDOM (Wide In Silico Docking On Malaria) addressed successfully in silico high-throughput screening  ... 
doi:10.2174/1871526510909030358 pmid:19519488 fatcat:3j4mcyrdqzcu5ha3wyyyehqm5i

Innovative in silico approaches to address avian flu using grid technology [article]

V. Vincent Breton, P. De Vlieger , Y.-M. Kim, D. Kim, H.Q. Nguyen, T. Solomonides, Y.-T. Wu, T. N. Hai
2008 arXiv   pre-print
on international grid infrastructures.  ...  For 3 years now, a collaboration of teams in Europe and Asia has been exploring some innovative in silico approaches to better tackle avian flu taking advantage of the very large computing resources available  ...  CURRENT USES OF GRID TECHNOLOGY FOR DRUG DISCOVERY ON AVIAN FLU In silico virtual screening In 2005, the WISDOM (Wide In Silico Docking On Malaria) addressed successfully in silico high-throughput screening  ... 
arXiv:0812.4341v1 fatcat:hlezycpo2fhdva723j3vgdatdi

Grid-Enabled High-Throughput In Silico Screening Against Influenza A Neuraminidase

Hurng-Chun Lee, Jean Salzemann, Nicolas Jacq, Hsin-Yen Chen, Li-Yung Ho, Ivan Merelli, Luciano Milanesi, Vincent Breton, Simon C. Lin, Ying-Ta Wu
2006 IEEE Transactions on Nanobioscience  
In the paper, we demonstrate the impact of a world-wide Grid infrastructure to efficiently deploy large scale virtual screening [2] to speed up the drug design process.  ...  Mobilizing thousands of CPUs on the Grid, the 6-weeks long high-throughput screening activity has fulfilled over 100 CPU years of computing power and produced around 600 Gigabytes of results on the Grid  ...  ACKNOWLEDGMENTS The authors express particular thanks to the site managers in EGEE, TWGrid, AuverGrid, BioinfoGRID for operational support, the LCG ARDA group for the technical support of DIANE, and the  ... 
doi:10.1109/tnb.2006.887943 pmid:17181029 fatcat:6abw4jzwarhkhbexridjdgbigu

AutoDock Gateway for Molecular Docking Simulations in Cloud Systems [chapter]

Zoltán Farkas, Péter Kacsuk, Tamás Kiss, Péter Borsody, Ákos Hajnal, Ákos Balaskó, Krisztián Karóczkai
2015 Cloud Computing with e-Science Applications  
WISDOM was the first large scale in silico docking experiment on public grid infrastructure.  ...  AutoDock is one example of a program which allows in silico modeling of intermolecular interactions. AutoDock is a suite of automated docking tools.  ... 
doi:10.1201/b18021-11 fatcat:ukz6lkplsvfenakzt7uco2eoce

Ab Initio potential grid based docking: From High Performance Computing to In Silico Screening

Marc R. de Jonge, H. Maarten Vinkers, Joop H. van Lenthe, Frits Daeyaert, Ian J. Bush, Huub J. J. van Dam, Paul Sherwood, Martyn F. Guest, Arno P. J. M. Siebes, Michael R. Berthold, Robert C. Glen, Ad J. Feelders
2007 AIP Conference Proceedings  
A large subregion of the crystal structure of Isocitrate Lyase, was selected as docking target.  ...  In contrast the same docking procedure, but using a classical pointcharge based potential, produces a number of additional incorrect binding poses, and does not recognize the correct pose as the best solution  ...  Acknowledgments Part of this work was carried out under the HPC-EUROPE Project (RII3-CT-2003-506079), with the support of the European Community Research Infrastructure Action under the FP6 Structure of  ... 
doi:10.1063/1.2793399 fatcat:o5nuyldxe5ghpjfenmogwdby6a

Assessment of the developmental success of Anopheles coluzzii larvae under different nutrient regimes: effects of diet quality, food amount and larval density

Patric Stephane Epopa, Hamidou Maiga, Domonbabele François de Sales Hien, Roch Kounbobr Dabire, Rosemary Susan Lees, Jeremie Giles, Frederic Tripet, Thierry Baldet, David Damiens, Abdoulaye Diabate
2018 Malaria Journal  
Jane Morris for discussions and in-depth reading of this manuscript. We thank Dr. Henri Vial for fruitful discussions, and Dr. Clotilde Claudel-Renard and Dr.  ...  EGEE-II is a project funded by the European Union under contract number INFSO-RI-031688. This publication was further supported by the New Partnership for Africa's Development (NEPAD), African Union.  ...  The WISDOM initiative successfully deployed large scale in silico docking on the European public EGEE grid infrastructure.  ... 
doi:10.1186/s12936-018-2530-z fatcat:nlobxtvlljhyxpb2rz4iml4hjy
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