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, 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},
   Year = {2007}
}