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Large Scale In Silico Screening on Grid Infrastructures
[article]
2006
arXiv
pre-print
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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
2007
Parallel Computing
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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
2007
Journal of Grid Computing
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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
2009
Malaria Journal
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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]
2021
arXiv
pre-print
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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
2007
Seventh IEEE International Symposium on Cluster Computing and the Grid (CCGrid '07)
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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]
2009
Grid Computing
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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
2008
IEEE Transactions on Information Technology in Biomedicine
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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
2006
Sixth IEEE International Symposium on Cluster Computing and the Grid (CCGRID'06)
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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
2009
Infectious Diseases - Drug Targets
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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]
2008
arXiv
pre-print
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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
2006
IEEE Transactions on Nanobioscience
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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]
2015
Cloud Computing with e-Science Applications
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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
2007
AIP Conference Proceedings
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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
2018
Malaria Journal
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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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