Supporting NAMD Application on the Grid Using GPE

Kluszczyński, Rafał; Bała, Piotr

doi:10.1007/978-3-540-68111-3_80

Cited by 4 publications

(4 citation statements)

References 5 publications

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“…Amongst other applications, the project also targeted the NAMD molecular dynamics package [43] and the AutoDock docking software. The Chemomentum environment also supports the creation and execution of workflows on Unicore resources.…”

Section: Related Workmentioning

confidence: 99%

Parameter Sweep Workflows for Modelling Carbohydrate Recognition

et al. 2010

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Carbohydrate recognition is a phenomenon critical to a number of biological functions in humans. Understanding the dynamic behaviour of oligosaccharides should help in the discovery of the mechanisms which lead to specific and selective recognition of carbohydrates by proteins. Computer programs which can provide insight into such biological recognition processes have significant potential to contribute to biomedical research if the results of the simulation can prove consistent with the outcome of conventional wet laboratory experiments. In order to validate these simulation tools and support their wider uptake by the bio-scientist research community, high-level easy to use integrated environments are required to run massively parallel simulation workflows. This paper describes how the ProSim Science Gateway, based on the WS-PGRADE Grid portal, has been created to execute and visualise the results of complex parameter sweep workflows for modelling carbohydrate recognition.T. Kiss (B) · G. Terstyanszky · N. Weingarten

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Section: Related Workmentioning

confidence: 99%

Parameter Sweep Workflows for Modelling Carbohydrate Recognition

et al. 2010

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“…The procedure is similar to that used by other workers. 15,[52][53][54][55][56][57][58][59] We took advantage of the InfiniBand (InfiniBand Trade Association, Beaverton, OR) capabilities of the Grid5000 clusters providing 100% Transfert_100 Transfert_200 Transfert_300 Transfert_400 Transfert_500 Transfert_600 Transfert_700 Transfert_800 Transfert_900 Transfert_1000 Transfert_1100 Transfert_1200 Transfert_1300 Transfert_1400 Transfert_1500 Transfert_1600 Transfert_1700 Transfert_1800 Transfert_1900 Transfert_2000 Transfert_2100 Local_100 Transfert_100 Transfert_200 Transfert_300 Transfert_400 Transfert_500 Transfert_600 Transfert_700 Transfert_800 Transfert_900 Transfert_1000 Transfert_1100 Transfert_1200 Transfert_1300 Transfert_1400 Transfert_1500 Transfert_1600 Transfert_1700 Transfert_1800 Transfert_1900 Transfert_2000 Transfert_2100 high throughput virtual screening on cluster grid Dovepress submit your manuscript | www.dovepress.com Dovepress efficiency for each node on which NAMD was running. The results of these calculations are shown in Table 1.…”

Section: Namd Final Refinementsmentioning

confidence: 99%

Efficiency of a hierarchical protocol for high throughput structure-based virtual screening on GRID5000 cluster grid

Ghemtio¹,

Jeannot²,

Maigret³

2010

OAB

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Most modern computational techniques in the drug discovery areas put demands on large computer resources. Grid computing offers a powerful alternative way of running computationally intensive applications. One field of the drug innovation process that can benefit greatly from the use of grid resources is the high-throughput virtual screening approach for docking huge chemical compound libraries into known protein-binding sites. The use of computational grids is the combination of computer resources from multiple administrative domains, heterogeneous, and geographically dispersed applications to a common task that requires a great number of computer-processing cycles or the need to process large amounts of data. This study detailed a screening campaign, on Grid5000 cluster grid computing infrastructure, concerning the ZINC database, from which a subset of ∼600,000 "drug-like" molecules was extracted, against three structures of the liver-X receptor β (LXR β). A funnel strategy was used for that purpose, starting from a fast but simple shape matching procedure and achieved with more complex molecular dynamics simulations. From a total of ∼91 million three-dimensional conformations which were generated at the beginning of the funnel and after intermediate filtering steps, the process ended with 45 putative hits. The GRID5000 is a highly reconfigurable, controllable, and monitorable experimental cluster grid, connecting nine sites geographically distributed in France, and featuring more than 3,200 processors and 5,700 cores. To hide the complexity of the grid system from the user, the GRID5000 has been used through the virtual screening manager for grid computing (VSM-G) platform, dedicated to in silico screening and to provide maximum computing power by using grid resources efficiently. The whole screening process required around 82 days (78 days of pre-processing and 3.6 days for the docking funnel itself) and utilized 3,144 nodes over nine sites. The use of grid infrastructures and hierarchical filtering protocol enable us to perform evaluations of the binding capabilities of millions of compounds on several conformations of a given target and propose that, with a low cost, most promising compounds for in vitro tests.

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“…In the last years, authors have developed gridbeans for bioinformatics tools like BLAST, NAMD or Clustal (Borcz et al, 2007;Kluszczyński and Bała, 2008;Kluszczyński and Bała, 2009). All mentioned gridbeans provide a graphical interface which makes possible to run the applications in an easy way.…”

Section: Application Gridbeansmentioning

confidence: 99%

“…Applications such as BLAST (Basic Local Alignment Search Tool), Clustal and NAMD (Not Another Molecular Dynamics) are widely used by the molecular biology scientists. Authors successfully supported them on the UNICORE Grid (Borcz et al, 2007;Kluszczyński and Bała, 2008;Kluszczyński and Bała, 2009). However, there has been noticed the need for the statistical tools to analyze data.…”

Section: Introductionmentioning

confidence: 99%

Statistical Analysis of Biomolecular Data Using Unicore Workflows

Borcz

Kluszczyński

Bała

2010

Proceedings of the First International Conference on Bioinformatics

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Nowadays the role of e-Science is important, especially in the area of life sciences. Experiments and their analysis are carried out in collaboration of many scientific groups from institutes located all over the world. Moreover, they work with immense amount of data which usually needs to be processed statistically. Therefore, the need for computing power is increasing. It usually can not be supplied by a standard laboratory. That is why e-Science makes use of grid technology. UNICORE (Uniform Interface to Computing Resources) is a middleware enabling access to the Grid resources in a seamless and secure way. In this paper we present UNICORE gridbean for statistical R environment which enables to process statistically data on the Grid. Being used as a part of more complex workflow task it can analyze results given by another applications and calculate needed statistics. By presenting example workflow constructed in UNICORE Rich Client application, authors show power of the Chemomentum workbench built on UNICORE Grid system.

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Supporting NAMD Application on the Grid Using GPE

Cited by 4 publications

References 5 publications

Parameter Sweep Workflows for Modelling Carbohydrate Recognition

Parameter Sweep Workflows for Modelling Carbohydrate Recognition

Efficiency of a hierarchical protocol for high throughput structure-based virtual screening on GRID5000 cluster grid

Statistical Analysis of Biomolecular Data Using Unicore Workflows

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