GaHMLC07jsw

J.I. Garzon, E. Huedo, R.S. Montero, I.M. Llorente, P. Chacon. Adaptation of a Multi-Resolution Docking Bioinformatics Application to the Grid. Journal of Software, 2(2):1-10, 2007.

Abstract

Rigid body fitting is the common way to interpret the 3D information contained in a electron microscopy (3DEM) low resolution density map in terms of its available 3D atomic resolution structural components. This fitting process, termed multi-resolution docking, consists in localizing atomic resolution structures into the 3D EM map by means of an exhaustive search of all possible relative rotations and translations. In addition to the cost of a single search, the necessity to carry out multiple searches with many different structures makes this problem appropriate for high performance computing (HPC). The Grid Computing paradigm provides such computing power for this type of resource-intensive scientific applications allowing the access to large resource pools conformed from shared assets of different centres or administration entities. Here, we present an efficient Grid approach for performing the multi-resolution docking searches. This approach has been designed over the GridWay Metascheduler. We show the suitability of the adaptation of the problem to the Grid paradigm. Results showing the high efficiency achieved are discussed together with the analysis of the performance obtained over the Grid testbed employed

Keywords

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

Contact

Eduardo Huedo
Ruben S. Montero
Ignacio M. Llorente

BibTex Reference

@article{GaHMLC07jsw,
   Author = {Garzon, J.I. and Huedo, E. and Montero, R.S. and Llorente, I.M. and Chacon, P.},
   Title = {Adaptation of a Multi-Resolution Docking Bioinformatics Application to the Grid},
   Journal = {Journal of Software},
   Volume = {2},
   Number = {2},
   Pages = {1--10},
   Year = {2007}
}