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GaHMLC07pdp

J.I. Garzon, E. Huedo, R.S. Montero, I.M. Llorente, P. Chacon. Grid Multi-Resolution Docking. In 15th EUROMICRO International Conference on Parallel, Distributed and Network-Based Processing (PDP 2007), Pages 3-10, February 2007.

Abstract

Detailed knowledge of macromolecular structure is essential for the understanding of how the cellular machines work. Rigid body fitting is the common way to interpret the information contained in a 3D electron microscope (3DEM) medium-low resolution map in terms of its available atomic structural components. This fitting process, termed multi-resolution docking, consists in localizing atomic resolution structures into the 3DEM map by means of an exhaustive search of all possible relative rotations and translations. This exhaustive search is a highly computing demanding process and several search queries are also typically needed to select good fitting structures. Here, we present a novel and efficient Grid approach for performing these docking searches. This approach has been designed over the Gridway meta-scheduler. Results showing the high efficiency achieved are discussed together with the corresponding analysis of the performance obtained. The experiments were conducted on a Grid testbed built up from resources inside EGEE (LCG version of the pre-WS Globus components), the European production-level grid infrastructure, and resources from a research testbed based on the Globus Toolkit 4 (Web services components)

Keywords

[ Gridway ] [ Grid ] [ Tic2003-01321 ] [ Egee ]

Contact

Eduardo Huedo
Ruben S. Montero
Ignacio M. Llorente

BibTex Reference

@InProceedings{GaHMLC07pdp,
   Author = {Garzon, J.I. and Huedo, E. and Montero, R.S. and Llorente, I.M. and Chacon, P.},
   Title = {Grid Multi-Resolution Docking},
   BookTitle = {15th EUROMICRO International Conference on Parallel, Distributed and Network-Based Processing (PDP 2007)},
   Pages = {3--10},
   Month = {February},
   Year = {2007}
}

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