A grid-aware approach to protein structure comparison

Authors:
Carlo Ferrari;Concettina Guerra;Giuseppe Zanotti
Affiliations:
Department of Information Engineering, University of Padova, via Gradenigo 6a, 35131 Padova, Italy;Department of Information Engineering, University of Padova, via Gradenigo 6a, 35131 Padova, Italy;Dip. Chimica Organica e Centro Studi Biopolimeri, Univ. of Padova, via Marzolo 1, Padova, Italy
Venue:
Journal of Parallel and Distributed Computing - High-performance computational biology
Year:
2003

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Abstract

This paper concentrates on the grid implementation of software tools for the comparison of protein structures. We have developed comparison algorithms based on indexing techniques that store transformation invariant properties of the 3D protein structures into tables. The method has large memory requirements and is computationally intensive. Furthermore, the dataset needs frequent updates as new proteins are added to the Protein Data Bank. Thus a significant advantage is obtained from a computational framework such as a grid. We report on a distributed implementation of the matching procedures on a grid using Globus MPI-CH, focusing on the data partition strategy to achieve good load balancing and to minimize the number of secondary memory accesses of the out-of-core computation.