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Grid Multi-Resolution Docking

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5 Author(s)
Garzon, J.L. ; Centro de Investigaciones Biologicas, CSIC, Madrid ; Huedo, E. ; Montero, R.S. ; Llorente, I.M.
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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)

Published in:

Parallel, Distributed and Network-Based Processing, 2007. PDP '07. 15th EUROMICRO International Conference on

Date of Conference:

7-9 Feb. 2007