Grid warehousing of molecular dynamics protein unfolding data

Frederic Stahl, Daniel Berrar, Candida Silva, J. Rui Rodrigues, Rui M M Brito, Werner Dubitzky

Research output: Chapter in Book/Report/Conference proceedingConference contribution

7 Citations (Scopus)

Abstract

With the increasing awareness of protein folding disorders, the explosion of genomic information, and the need for efficient ways to predict protein structure, protein folding and unfolding has become a central issue in molecular sciences research. Molecular dynamics computer simulations are increasingly employed to understand the folding and unfolding of proteins. Running protein unfolding simulations is computationally expensive and finding ways to enhance performance is a grid issue on its own. However, more and more groups run such simulations and generate a myriad of data, which raises new challenges in managing and analyzing these data. Because the vast range of proteins researchers want to study and simulate, the computational effort needed to generate data, the large data volumes involved, and the different types of analyses scientists need to perform, it is desirable to provide a public repository allowing researchers to pool and share protein unfolding data. This paper describes efforts to provide a grid-enabled data warehouse for protein unfolding data. We outline the challenge and present first results in the design and implementation of the data warehouse.

Original languageEnglish
Title of host publication2005 IEEE International Symposium on Cluster Computing and the Grid, CCGrid 2005
Pages496-503
Number of pages8
Volume1
DOIs
Publication statusPublished - 2005
Externally publishedYes
Event2005 IEEE International Symposium on Cluster Computing and the Grid, CCGrid 2005 - Cardiff, Wales, United Kingdom
Duration: 2005 May 92005 May 12

Other

Other2005 IEEE International Symposium on Cluster Computing and the Grid, CCGrid 2005
CountryUnited Kingdom
CityCardiff, Wales
Period05/5/905/5/12

Fingerprint

Molecular dynamics
Proteins
Protein folding
Data warehouses
Explosions
Computer simulation

ASJC Scopus subject areas

  • Engineering(all)

Cite this

Stahl, F., Berrar, D., Silva, C., Rodrigues, J. R., Brito, R. M. M., & Dubitzky, W. (2005). Grid warehousing of molecular dynamics protein unfolding data. In 2005 IEEE International Symposium on Cluster Computing and the Grid, CCGrid 2005 (Vol. 1, pp. 496-503). [1558594] https://doi.org/10.1109/CCGRID.2005.1558594

Grid warehousing of molecular dynamics protein unfolding data. / Stahl, Frederic; Berrar, Daniel; Silva, Candida; Rodrigues, J. Rui; Brito, Rui M M; Dubitzky, Werner.

2005 IEEE International Symposium on Cluster Computing and the Grid, CCGrid 2005. Vol. 1 2005. p. 496-503 1558594.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Stahl, F, Berrar, D, Silva, C, Rodrigues, JR, Brito, RMM & Dubitzky, W 2005, Grid warehousing of molecular dynamics protein unfolding data. in 2005 IEEE International Symposium on Cluster Computing and the Grid, CCGrid 2005. vol. 1, 1558594, pp. 496-503, 2005 IEEE International Symposium on Cluster Computing and the Grid, CCGrid 2005, Cardiff, Wales, United Kingdom, 05/5/9. https://doi.org/10.1109/CCGRID.2005.1558594
Stahl F, Berrar D, Silva C, Rodrigues JR, Brito RMM, Dubitzky W. Grid warehousing of molecular dynamics protein unfolding data. In 2005 IEEE International Symposium on Cluster Computing and the Grid, CCGrid 2005. Vol. 1. 2005. p. 496-503. 1558594 https://doi.org/10.1109/CCGRID.2005.1558594
Stahl, Frederic ; Berrar, Daniel ; Silva, Candida ; Rodrigues, J. Rui ; Brito, Rui M M ; Dubitzky, Werner. / Grid warehousing of molecular dynamics protein unfolding data. 2005 IEEE International Symposium on Cluster Computing and the Grid, CCGrid 2005. Vol. 1 2005. pp. 496-503
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