Title: A parallel protein surface reconstruction system

Authors: Ivan Merelli, Alessandro Orro, Daniele D'Agostino, Andrea Clematis, Luciano Milanesi

Addresses: Institute for Biomedical Technologies, National Research Council, Segrate (Milan), Italy. ' Institute for Biomedical Technologies, National Research Council, Segrate (Milan), Italy. ' Institute for Applied Mathematics and Information Technology, National Research Council, Genova, Italy. ' Institute for Applied Mathematics and Information Technology, National Research Council, Genova, Italy. ' Institute for Biomedical Technologies, National Research Council, Segrate (Milan), Italy

Abstract: In this paper we propose a parallel system for protein surface reconstruction based on techniques of computational geometry. The advantage of our modelling system is the production of both superficial and volumetric description of proteins. This is very important in protein analysis from the functional point of view, because many binding sites are buried inside the macromolecule. However the amount of data to process, both in the volume modelling and in extraction phase, may be huge, in proportion to the selected resolution of the output. For this reason the parallel implementation of the system represents a fundamental aspect in reducing the processing time.

Keywords: protein modelling; parallel mesh simplification; parallel isosurface extraction; Connolly volumetric correction; bioinformatics; protein surface reconstruction.

DOI: 10.1504/IJBRA.2008.019572

International Journal of Bioinformatics Research and Applications, 2008 Vol.4 No.3, pp.221 - 239

Available online: 17 Jul 2008 *

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