This Article 
 Bibliographic References 
 Add to: 
Molecular Surface Abstraction
November/December 2007 (vol. 13 no. 6)
pp. 1608-1615
In this paper we introduce a visualization technique that provides an abstracted view of the shape and spatio-physico-chemical properties of complex molecules. Unlike existing molecular viewing methods, our approach suppresses small details to facilitate rapid comprehension, yet marks the location of significant features so they remain visible. Our approach uses a combination of filters and mesh restructuring to generate a simplified representation that conveys the overall shape and spatio-physico-chemical properties (e.g. electrostatic charge). Surface markings are then used in the place of important removed details, as well as to supply additional information. These simplified representations are amenable to display using stylized rendering algorithms to further enhance comprehension. Our initial experience suggests that our approach is particularly useful in browsing collections of large molecules and in readily making comparisons between them.

[1] N. A. Baker, D. Sept, S. Joseph, M. J. Holst, and J. A. McCammon, Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. National Academy of Sciences, 98 (18): 10037–10041, Aug 2001.
[2] H. M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T. N. Bhat, H. Weissig, I. N. Shindyalov, and P. E. Bourne, The protein data bank. Nucleic Acids Research, 28 (1): 235–242, 2000.
[3] J.-D. Boissonnat, O. Devillers, J. Duquesne, and M. Yvinec, Computing connolly surfaces. J. Molecular Graphics, 12 (1): 61–62, March 1994.
[4] M. Chapman, Mapping the surface properties of macromolecules. Protein Science, 2 (3): 459–469, 1993.
[5] H.-L. Cheng and X. Shi, Quality mesh generation for molecular skin surfaces using restricted union of balls. In Proceedings IEEE Visualization Conference, 2005.
[6] M. Connolly, Solvent-accessible surfaces of proteins and nucleic acids. Science, 221 (4612): 709–13, August19, 1983 1983.
[7] M. L. Connolly, The molecular surface package. J. Molecular Graphics, 11 (2): 139–141, June 1993.
[8] M. L. Connolly, Molecular surfaces: A review. Network Science online article , 1996.
[9] D. DeCarlo, A. Finkelstein, and S. Rusinkiewicz, Interactive rendering of suggestive contours with temporal coherence. In Proceedings NPAR, pages 15–24, 145, 2004.
[10] D. DeCarlo, A. Finkelstein, S. Rusinkiewicz, and A. Santella, Suggestive contours for conveying shape. In Proceedings SIGGRAPH, pages 848–855, 2003.
[11] W. DeLano, The PyMOL molecular graphics system, 2002.
[12] K. Fujiwara, Eigenvalues of laplacians on a closed riemannian manifold and its nets. AMS, pages 2585–2594, 1995.
[13] T. Goddard, C. Huang, and T. Ferrin, Software extensions to ucsf chimera for interactive visualization of large molecular assemblies. Structure, 13: 473–482, March 2005.
[14] R. Gonzalez and R. E. Woods, Digital Image Processing. Prentice Hall, 2002.
[15] D. Goodsell and A. Olsen, Molecular illustration in black and white. J. Molecular Graphics, 10 (4): 235–40, 1992.
[16] D. S. Goodsell, Visual methods from atoms to cells. Structure, 13: 347–354, March 2005.
[17] G. Gorla, V. Interrante, and G. Sapiro, Texture synthesis for 3d shape representation. IEEE Transactions on Visualization and Computer Graphics, 9 (4): 512–524, 2003.
[18] G. Grigoryan and P. Rheingans, Probabilistic Surfaces: Point Based Primitives to Show Surface Uncertainty. In Proceedings IEEE Visualization, 2002.
[19] M. Hendlich, F. Rippmann, and G. Barnickel, LIGSITE: automatic and efficient detection of potential small molecule-binding sites in proteins. J. Molecular Graphics and Modelling, 15 (6): 359–363, 1997.
[20] H. Landis, Production ready global illumination. In Siggraph Course Notes, 2002.
[21] C. Lee and A. Varshney, Representing thermal vibrations and uncertainty in molecular surfaces. In SPIE Conference on Visualization and Data Analysis, 2002.
[22] C. H. Lee, X. Hao, and A. Varshney, Light Collages: Lighting Design for Effective Visualization. In IEEE Visualization, pages 281–288, 2004.
[23] D. P. Luebke, A developer's survey of polygonal simplification algorithms. IEEE CG&A, 21 (3): 24–35, 2001.
[24] A. Nicholls, R. Bharadwaj, and B. Honig, Grasp: Graphical representation and analysis of surface properties. In 37th Meeting of the Biophysical Society, volume 64, page A166, 1993.
[25] J. W. Nissink, C. Murray, M. Hartshorn, M. Verdonk, J. Cole, and R. Taylor, A new test set for validating predictions of protein-ligand interaction. Proteins: Structure, Function and Genetics, 49 (4): 457–471, 2002.
[26] M. Pauly, R. Keiser, and M. Gross, Multi-scale Feature Extraction on Point-Sampled Surfaces. Comp. Graphics Forum, 22 (3): 281–289, 2003.
[27] E. F. Pettersen, T. D. Goddard, C. C. Huang, G. S. Couch, D. M. Greenblatt, E. C. Meng, and T. E. Ferrin, UCSF Chimera - a visualization system for exploratory research and analysis. Journal of Computational Chemistry, 25 (13): 1605 – 1612, 2004.
[28] M. F. Sanner, A component-based software environment for visualizing large macromolecular assemblies. Structure, 3 (3): 447–462, Mar 2005.
[29] M. F. Sanner, A. J. Olson, and J.-C. Spehner, Fast and robust computation of molecular surfaces. In SCG '95: Proceedings of the eleventh annual symposium on Computational geometry, pages 406–407, 1995.
[30] R. Schmidt, C. Grimm, and B. Wyvill, Interactive decal compositing with discrete exponential maps. ACM Transactions on Graphics, 25 (3): 603–613, 2006.
[31] J. Schmidt-Ehrenberg, D. Baum, and H. C. Hege, Visualizing dynamic molecular conformations. In Proceedings IEEE Visualization, pages 235–242, 2002.
[32] F. B. Sheinerman, R. Norel, and B. Honig, Electrostatic aspects of proteinprotein interactions (review). Current Opinion in Structural Biology, 10 (2): 153–159, 2000.
[33] G. R. Smith and M. J. E. Sternberg, Prediction of protein-protein interactions by docking methods (review). Current Opinion in Structural Biology, 12 (1): 28–35, Feb 2002.
[34] M. Tarini, P. Cignoni, and C. Montani, Ambient occlusion and edge cueing for enhancing real time molecular visualization. IEEE Transactions on Visualization and Computer Graphics, 12 (5): 1237–1244, 2006.
[35] J. Tate, Molecular visualization. In P. Bourne and H. Weissig, editors, Structural Bioinformatics, chapter 23. Wiley-Liss, 2003.
[36] G. Taubin, A signal processing approach to fair surface design. In Proceedings of SIGGRAPH 95, pages 351–358, Aug. 1995.
[37] G. Taubin, Geometric signal processing on polygonal meshes. In EURO-GRAPHICS - State of the Art Reports, 2000.
[38] C. Tomasi and R. Manduchi, Bilateral filtering for gray and color images. In ICCV, pages 839–846, 1998.
[39] A. Varshney and F. P. Brooks, Jr., Fast analytical computation of Richard's smooth molecular surface. In Proceedings IEEE Visualization, pages 300–307, 1993.

Index Terms:
molecular surfaces, molecular visualization, surfaces, textures, cartographic labeling
Gregory Cipriano, Michael Gleicher, "Molecular Surface Abstraction," IEEE Transactions on Visualization and Computer Graphics, vol. 13, no. 6, pp. 1608-1615, Nov.-Dec. 2007, doi:10.1109/TVCG.2007.70578
Usage of this product signifies your acceptance of the Terms of Use.