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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 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  ...  WISDOM, a first virtual screening initiative on grid infrastructures WISDOM is an initiative for a World-wide In Silico Docking On Malaria.  ... 
doi:10.1007/s10723-007-9085-5 fatcat:ebxn7dfkxve6pgeo7tv4mptkie

Grid enabled virtual screening against malaria Grid enabled virtual screening against malaria

N Jacq, J Salzemann, F Jacq, Yannick Legre, E Medernach, Johan Montagnat, A Maass, M Reichstadt, H Schwichtenberg, M Sridhar, N Jacq, J Salzemann (+12 others)
2008 Journal of Grid Computing   unpublished
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 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  ...  WISDOM, a first virtual screening initiative on grid infrastructures WISDOM is an initiative for a World-wide In Silico Docking On Malaria.  ... 
fatcat:fhcgwmcm6jc65kxcx2txqkkq6u

Grid-Added Value to Address Malaria

V. Breton, N. Jacq, V. Kasam, M. Hofmann-Apitius
2008 IEEE Transactions on Information Technology in Biomedicine  
And we propose to use the grid technology to enable such a world wide "open source" like collaboration.  ...  Through this paper, we call for a distributed, internet-based collaboration to address one of the worst plagues of our present world, malaria.  ...  The computing resources of a grid are also shared and can be mobilised on demand so as to enable very large scale genomics comparative analysis and virtual screening.  ... 
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)  
And we propose to use the grid technology to enable such a world wide "open source" like collaboration.  ...  Through this paper, we call for a distributed, internet-based collaboration to address one of the worst plagues of our present world, malaria.  ...  The computing resources of a grid are also shared and can be mobilised on demand so as to enable very large scale genomics comparative analysis and virtual screening.  ... 
doi:10.1109/ccgrid.2006.1630933 fatcat:qk2345didzexzepqoyhlr7eowy

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.  ...  In 2005 and 2006, we have been able to deploy large scale in silico docking within the framework of the WISDOM initiative against Malaria and Avian Flu requiring about 105 years of CPU on the EGEE, Auvergrid  ...  This paper has presented pioneering activities in the field of grid enabled virtual screening against neglected and emerging diseases in Europe.  ... 
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  
These achievements demonstrated the relevance of large scale grids for the virtual screening by molecular docking.  ...  In 2005 and 2006, we have been able to deploy large scale virtual docking within the framework of the WISDOM initiative against malaria and avian influenza requiring about 100 years of CPU on the EGEE,  ...  The Enabling Grids for E-sciencE (EGEE) project is co-funded by the European Commission under contract INFSO-RI-031688. Auvergrid is a project funded by the Conseil Regional d'Auvergne.  ... 
doi:10.1016/j.parco.2007.02.010 fatcat:4zghjxovejesfdwl25gdirpoie

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)  
We screened ZINC database against four targets implicated in malaria.  ...  Computational grids are solutions for several biological applications like virtual screening or molecular dynamics where large amounts of computing power and storage are required.  ...  In silico screening of chemical compounds against a particular target is termed as virtual screening.  ... 
doi:10.1109/ccgrid.2007.66 dblp:conf/ccgrid/KasamSJMB07 fatcat:qy2u76mvl5dgbbbppiyfpvhyxi

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  
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  ...  Despite continuous efforts of the international community to reduce the impact of malaria on developing countries, no significant progress has been made in the recent years and the discovery of new drugs  ...  The Enabling Grids for E-sciencE (EGEE) project is co-funded by the European Commission under contract INFSO-RI-031688. Auvergrid is a project funded by the Conseil Regional d'Auvergne.  ... 
doi:10.1186/1475-2875-8-88 pmid:19409081 pmcid:PMC2691744 fatcat:dbqivtpnojcfzas67rjvuhll6u

OpenZika: An IBM World Community Grid Project to Accelerate Zika Virus Drug Discovery

Sean Ekins, Alexander L. Perryman, Carolina Horta Andrade, David Joseph Diemert
2016 PLoS Neglected Tropical Diseases  
This will enable the identification of new candidates that can then be tested in vitro, to advance the discovery and development of new antiviral drugs against the Zika virus.  ...  OpenZika is an IBM World Community Grid Project that uses distributed computing on millions of computers and Android devices to run docking experiments, in order to dock tens of millions of drug-like compounds  ...  Acknowledgments We kindly acknowledge all our collaborators on this project (http://openzika.ufg.br), the wonderful ongoing support and encouragement of the IBM World Community Grid team, and the community  ... 
doi:10.1371/journal.pntd.0005023 pmid:27764115 pmcid:PMC5072634 fatcat:3lt6yfadnbgs7ntizazyv5atby

Wisdom [chapter]

Vincent Breton, Doman Kim, Giulio Rastelli
2009 Grid Computing  
Grid-Enabled Virtual Screening 14.2.2 Virtual screening is about selecting in silico the best candidate drugs acting on a given target protein [2] .  ...  Virtual screening is the process that screens the chemical compounds in silico against a target.  ... 
doi:10.1201/9781420067682-c14 fatcat:ugdxhna5pnhq7fz7ymtxdw7giq

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.  ...  Encouraged by the success of the first EGEE biomedical data challenge against malaria (WISDOM) [1], the second data challenge battling avian flu kicked off in April 2006 to identify new drugs for the potential  ...  of the in silico high-throughput screening (HTS) environment based on what has been learnt in the previous challenge against Malaria (WISDOM) [7] ; the other is to test another environment which enables  ... 
doi:10.1109/tnb.2006.887943 pmid:17181029 fatcat:6abw4jzwarhkhbexridjdgbigu

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  
The computing resources of a grid are also shared and can be mobilized on demand so as to enable very large-scale genomics comparative analysis and virtual screening.  ...  Beyond virtual screening, the grid technology provides the collaborative IT environment to enable the coupling between molecular biology research and goal-oriented field work [189] .  ...  Authors' contributions All authors contributed to the analysis of the current status on the in silico storage and organization of malaria genomics, post-genomics data and antimalaria chemical information  ... 
doi:10.1186/s12936-018-2530-z fatcat:nlobxtvlljhyxpb2rz4iml4hjy

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  
Grids were used to study the impact of mutations on the effectiveness of existing drugs against H5N1 and to find potentially new leads active on mutated strains.  ...  Grids allow also the integration of distributed data in a completely secured way.  ...  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
Grids were used to study the impact of mutations on the effectiveness of existing drugs against H5N1 and to find potentially new leads active on mutated strains.  ...  Grids allow also the integration of distributed data in a completely secured way.  ...  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

A Virtual Screen Discovers Novel, Fragment-Sized Inhibitors of Mycobacterium tuberculosis InhA

Alexander L. Perryman, Weixuan Yu, Xin Wang, Sean Ekins, Stefano Forli, Shao-Gang Li, Joel S. Freundlich, Peter J. Tonge, Arthur J. Olson
2015 Journal of Chemical Information and Modeling  
Virtual screening experiments versus InhA in the GO Fight Against Malaria project (GO FAM) were designed to discover new scaffolds that display base stacking interactions with the NAD cofactor.  ...  GO FAM experiments included targets from other pathogens, including Mtb, when they had structural similarity to a malaria target.  ...  We thank Sargis Dallakyan for maintaining the server that was used to submit these virtual screens to the GO FAM project and to receive the results from it.  ... 
doi:10.1021/ci500672v pmid:25636146 pmcid:PMC4386068 fatcat:msoyu5a5cbawzokf33xjc7nhmm
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