Digital Library of the European Council for Modelling and Simulation

Title:	Modelling The Response Of Bambara Groundnut: A Key Underutilised Crop In Agricultural Systems
Authors:	Asha Karunaratne, Neil Crout, Sayed Azam-Ali, Sean Mayes, Pasquale Steduto, Gabriella Izzi
Published in:	(2009).ECMS 2009 Proceedings edited by J. Otamendi, A. Bargiela, J. L. Montes, L. M. Doncel Pedrera. European Council for Modeling and Simulation. doi:10.7148/2009 ISBN: 978-0-9553018-8-9 23^rd European Conference on Modelling and Simulation, Madrid, June 9-12, 2009
Citation format:	Karunaratne, A., Crout, N., Azam-Ali, S., Mayes, S., Steduto, P., & Izzi, G. (2009). Modelling The Response Of Bambara Groundnut: A Key Underutilised Crop In Agricultural Systems. ECMS 2009 Proceedings edited by J. Otamendi, A. Bargiela, J. L. Montes, L. M. Doncel Pedrera (pp. 841-847). European Council for Modeling and Simulation. doi:10.7148/2009-0841-0847
DOI:	http://dx.doi.org/10.7148/2009-0841-0847
Abstract:	Proteins play a vital role in maintaining the balance of bodily functions in all living beings. However their functional properties are difficult to predict since they depend not only on the sequence of constituent amino acids but also on the 3D folding of the protein. This paper presents a new statistical method for extraction of surface atoms of a protein. The method is based on space-voxelisation and generalizes our previous deterministic method by repeating the surface extraction process for various orientations of a protein; so as to achieve a statistical consensus about surface atoms. Based on the experimental study we have established an optimal range of values of voxel occupancy for the selection of surface atoms; with optimality defined as a maximum coincidence of extracted surface atoms from the protein presented to the algorithm in 13 different orientations. The results show that the voxel occupancy threshold of between >40% and >50% allows our algorithm to extract surface atoms with high degree of confidence.
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