Adaptation of a Multi-Resolution Docking Bioinformatics Application to the Grid J.I. Garz´ on Centro de Investigaciones Biol´ ogicas-CSIC 28040 Madrid (Spain) garzon@cib.csic.es E. Huedo Facultad de Inform´ atica, Universidad Complutense 28040 Madrid (Spain) ehuedo@fdi.ucm.es R.S. Montero Facultad de Inform´ atica, Universidad Complutense 28040 Madrid (Spain) rubensm@dacya.ucm.es I.M. Llorente Facultad de Inform´ atica, Universidad Complutense 28040 Madrid (Spain) llorente@dacya.ucm.es P. Chac´ on Centro de Investigaciones Biol´ ogicas-CSIC 28040 Madrid (Spain) pablo@cib.csic.es 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 pro- cess, 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 struc- tures 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 perform- ing 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 Based on “Grid Multi-Resolution Docking”, by Garzon, J.I., Huedo, E., Montero, R.S., et al. which appeared in the proceedings of the Parallel, Distributed and Network-Based Processing, 2007, PDP 07, 15th Euromicro International Conference, Naples, Italy, Feb. 2007. c 2007. This research was supported by Ministerio de Ciencia y Tecnolog´ ıa through the research grants TIC2003-01321 and BPU2004-01282, and also by the Fundaci´ on BBVA. This work makes use of results produced by the Enabling Grids for E-sciencE project, a project co-funded by the European Commission (under contract number INFSO-RI-031688) through the Sixth Framework Programme. EGEE brings together 91 partners in 32 countries to provide a seamless Grid infrastructure available to the European research community 24 hours a day. Full information is available at http://www.eu-egee.org. 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. I. I NTRODUCTION Detailed knowledge of macromolecular structure is es- sential for the understanding of how the cellular machines work. Despite of the explosive growth of research in structural biology in last decades, the atomic resolution access to large macromolecular complexes involved in the main cellular functions is still rather limited. Elec- tron microscopy (EM) techniques are able to capture such large macromolecules in diverse near-physiological conditions [1]. Unfortunately, the resolution that can be obtained by EM is limited to low medium resolutions (10- 20 ˚ A). However, it is possible to achieve the atomic detail of the structure by localizing available atomic resolution components into the 3D EM low resolution map of a macromolecule. This is a complicated jigsaw puzzle in which the low resolution 3D EM density map of a macro- molecule acts as a fuzzy frame to guide the assemblage of interlocking atomic-resolution pieces. When complete, this jigsaw puzzle produces a near-atomic detail picture of the entire macromolecule. Thus, by solving this puzzle we can have access to a better understanding of the inner JOURNAL OF SOFTWARE, VOL. 2, NO. 2, AUGUST 2007 1 © 2007 ACADEMY PUBLISHER