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International Journal of Biomedical Imaging
Volume 2010, Article ID 923780, 9 pages
Research Article

Molecular Surface Mesh Generation by Filtering Electron Density Map

Communications and Remote Sensing Laboratory, Catholic University of Louvain, B-1348 Louvain-la-Neuve, Belgium

Received 25 September 2009; Revised 23 November 2009; Accepted 6 January 2010

Academic Editor: Guo Wei

Copyright © 2010 Joachim Giard and Benoît Macq. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.


Bioinformatics applied to macromolecules are now widely spread and in continuous expansion. In this context, representing external molecular surface such as the Van der Waals Surface or the Solvent Excluded Surface can be useful for several applications. We propose a fast and parameterizable algorithm giving good visual quality meshes representing molecular surfaces. It is obtained by isosurfacing a filtered electron density map. The density map is the result of the maximum of Gaussian functions placed around atom centers. This map is filtered by an ideal low-pass filter applied on the Fourier Transform of the density map. Applying the marching cubes algorithm on the inverse transform provides a mesh representation of the molecular surface.