JOURNAL OF SOFTWARE (JSW)
ISSN : 1796-217X
Volume : 2    Issue : 2    Date : August 2007

Adaptation of a Multi-Resolution Docking Bioinformatics Application to the Grid
José Ignacio Garzón, Eduardo Huedo, Rubén S. Montero, Ignacio M. Llorente, and Pablo Chacón
Page(s): 1-10
Full Text:
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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.

Index Terms
Multi-resolution docking; Grid computing; Grid application.