Virtual screening on large scale grids

Jacq, Nicolas; Breton, Vincent; Chen, Hsin-Yen; Ho, Li-Yung; Hofmann, Martin; Kasam, Vinod; Lee, Hurng-Chun; Legré, Yannick; Lin, S. C.; Maaí, Astrid; Medernach, Emmanuel; Merelli, Ivan; Milanesi, Luciano; Rastelli, Giulio; Reichstadt, Matthieu; Salzemann, Jean; Schwichtenberg, Horst; Wu, Ying‐Ta; Zimmermann, Marc

doi:10.1016/j.parco.2007.02.010

Cited by 27 publications

(18 citation statements)

References 30 publications

(36 reference statements)

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“…For examples, the molecular modeling for drug discovery was demonstrated by the WISDOM (Wide In Silico Docking on Malaria) and Virtual Laboratory and Opal activities [8][9][10][11][12]. The Virtual Laboratory and Opal use Nimrod-G which has the advantage of the Globus Toolkit and web service description language (WSDL) file to implement the Grid service-based platform [8].…”

Section: Related Workmentioning

confidence: 99%

“…In the first large-scale EGEE Biomed Data Challenge on the Grid [9], DIANE was used as an alternative approach to WISDOM scripts to manage millions of docking jobs on the Grid [9,10]. To compare with the large-scale job submission scripts, it has been shown that using the masterworker job-pulling model and the automatic failure recovery mechanism built into DIANE, one can increase the overall efficiency by 38% [9].…”

Section: Dianementioning

confidence: 99%

“…Those computing jobs are managed by GAP/DIANE to distribute the Grid computing workers to the Grid. The computing results are managed by AMGA metadata catalogue to store on the storage elements were employed in 4 weeks for Avian Flu Data Challenge (DC) in 2005 [9,10].…”

Section: Introductionmentioning

confidence: 99%

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GVSS: A High Throughput Drug Discovery Service of Avian Flu and Dengue Fever for EGEE and EUAsiaGrid

et al. 2010

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In the study of Biomedicines, molecular docking simulation is a common method for predicting potential interacting complexes of small molecules in protein binding sites. However, it is a time-consuming process to search exhaustively all correct conformations of a compound. This study demonstrates how massive molecular docking benefit from state-of-the-art Grid technology. Providing intensive computing power and effective data management, the production e-infrastructure (such as EGEE and EUAsiaGrid) enables opportunities for in-silico drug discovery on the neglected and emerging diseases, for instance, avian influenza and dengue fever. In this study, Grid Application Platform (GAP) and GAP-enabled Virtual Screening Service (GVSS) were developed with the docking engine of the Autodock 3.0.5. A JAVA-based graphical user interface and the GAP allow end-users to specify target and compound library, set up docking parameters, monitor docking jobs and computing resources, visualize and refine docking results, and finally download the final results. To provide a more user-friendly Grid service, GVSS was designed for conducting large-scale molecular docking more easily.

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Section: Related Workmentioning

confidence: 99%

Section: Dianementioning

confidence: 99%

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GVSS: A High Throughput Drug Discovery Service of Avian Flu and Dengue Fever for EGEE and EUAsiaGrid

et al. 2010

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“…For example, users from different parts of the world, including rural and remote areas, can utilize e-Infrastructures and have access to high-quality research resources, such as specialized instruments in bioinformatics or meteorological data for environmental sciences (Jacq et al, 2007). The availability of bandwidth has hampered African scientific communities from reaching similar benefits, but this is now rapidly changing as the UbuntuNet network's (AfricaConnect, 2014) interconnections unroll across the African continent.…”

Section: Introductionmentioning

confidence: 99%

“…Along the same lines, the Wide In-Silico Docking of Malaria (WISDOM) project aimed to develop high throughput virtual screening docking-based in-silico drug discovery platforms for neglected and emergent diseases supported by Grid computing (Jacq et al, 2007;Breton et al, 2008). EELA has enabled Latin American countries to take part in global scientific data challenges and to propose related projects, both to the benefit of Latin American scientists.…”

Section: Introductionmentioning

confidence: 99%

A study on the state-of-the-art of e-Infrastructures uptake in Africa

et al. 2015

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e-Science is a pioneering method that uses integrated collections of Information and Communication Technologies (ICTs), or e-Infrastructures, to enable scientists across the world to collaboratively work on more and more ambitious projects. Have advances and access to ICTs enabled African e-Infrastructure development? This paper aims to understand the current state of e-Infrastructure uptake in Africa and present some of these initiatives across the African continent by exploring the current landscape emerging from a survey of early consumers. These initiatives are discussed in terms of key projects and user communities that they are addressing. In line with wider perceptions that e-Infrastructures will re-shape the ways research is performed, this study yielded 34 current or planned e-Infrastructure projects across 13 African countries addressing a range of research domains, and identified 7 user communities across these disciplines. Our findings suggest that the African research community is increasingly interested and involved in e-Infrastructure development activities in response to the issue of limited access to dedicated global research and education resources. The study can contribute to the ongoing discussion on how e-Infrastructures can positively promote the research, technological development and innovation potential of developing countries.

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Design and Discovery of Plasmepsin II Inhibitors Using an Automated Workflow on Large‐Scale Grids

Degliesposti

Kasam

Costa³

et al. 2009

ChemMedChem

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Novel and potent inhibitors of Plasmodium falciparum plasmepsin II were identified by post-processing the results of a docking screening with BEAR, a recently reported procedure for the refinement and rescoring of docked ligands in virtual screening. FRET substrate degradation assays performed on the 30 most promising compounds resulted in 26 inhibitors with IC(50) values ranging from 4.3 nM to 1.8 microM.Herein we report the discovery of novel and potent inhibitors of Plasmodium falciparum plasmepsin II using GRID computing infrastructures. These compounds were identified by post-processing the results of a large docking screen of commercially available compounds using an automated procedure based on molecular dynamics refinement and binding free-energy estimation using MM-PBSA and MM-GBSA. Among the best-scored compounds, four highly populated and promising chemical classes were identified: N-alkoxyamidines, guanidines, amides, and ureas and thioureas. Thirty hit compounds representative of each class were selected on the basis of their favourable binding free energies and molecular interactions with key active site residues. These were experimentally validated using an inhibition assay based on FRET substrate degradation. Remarkably, 26 of the 30 tested compounds proved to be active as plasmepsin II inhibitors, with IC(50) values ranging from 4.3 nM to 1.8 microM.

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Virtual screening on large scale grids

Cited by 27 publications

References 30 publications

GVSS: A High Throughput Drug Discovery Service of Avian Flu and Dengue Fever for EGEE and EUAsiaGrid

GVSS: A High Throughput Drug Discovery Service of Avian Flu and Dengue Fever for EGEE and EUAsiaGrid

A study on the state-of-the-art of e-Infrastructures uptake in Africa

Design and Discovery of Plasmepsin II Inhibitors Using an Automated Workflow on Large‐Scale Grids

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