Back to Search Start Over

Adaptation of a Multi-Resolution Docking Bioinformatics Application to the Grid

Authors :
Rubén S. Montero
Ignacio M. Llorente
José Ignacio Garzón
Eduardo Huedo
Pablo Chacón
Source :
Journal of Software. 2
Publication Year :
2007
Publisher :
International Academy Publishing (IAP), 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.

Details

ISSN :
1796217X
Volume :
2
Database :
OpenAIRE
Journal :
Journal of Software
Accession number :
edsair.doi...........8f3c5b6b54b7ea8bcd34afee4696922c
Full Text :
https://doi.org/10.4304/jsw.2.2.1-10