Voronoi-based extraction and visualization of molecular paths

IEEE Transactions on Visualization and Computer Graphics

Volumn 17, Issue 12, 2011, Pages 2025-2034

  Lindow, Norbert ^a   Baum, Daniel ^a   Hege, Hans Christian ^a  

^a ZUSE INSTITUTE BERLIN   (Germany)

Author keywords

data filtering; geometry based techniques; Molecular visualization; view dependent visualization

Indexed keywords

DATA FILTERING; FILTERING METHOD; GEOMETRY-BASED TECHNIQUES; INTERACTIVE VISUALIZATIONS; MOLECULAR SURFACES; MOLECULAR VISUALIZATION; SKIN SURFACES; VIEW DEPENDENT VISUALIZATION; VISUAL ANALYSIS; VISUAL INSPECTION; VISUAL TRACKING; VORONOI DIAGRAMS;

BEHAVIORAL RESEARCH; BINDING SITES; LIGHT SOURCES; MOLECULES; USER INTERFACES; VISUALIZATION;

DATA VISUALIZATION;

PROTEIN;

ALGORITHM; ARTICLE; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER GRAPHICS; COMPUTER SIMULATION; METABOLISM; PROTEIN DOMAIN; SURFACE PROPERTY;

ALGORITHMS; BINDING SITES; COMPUTER GRAPHICS; COMPUTER SIMULATION; MODELS, MOLECULAR; PROTEIN INTERACTION DOMAINS AND MOTIFS; PROTEINS; SURFACE PROPERTIES;

EID: 80855130019     PISSN: 10772626     EISSN: None     Source Type: Journal    
DOI: 10.1109/TVCG.2011.259     Document Type: Article

References (49)

1. OpenGL Webseite, 2009. http://www.opengl.org/.
2. OpenMP Webseite, 2009. http://www.openmp.org/.
3. F. Aurenhammer. Power diagrams: properties, algorithms and applications. SIAM J. Comput., 16:78-96, February 1987. (Pubitemid 17526776)
4. C. Bajaj, A. Gillette, and S. Goswami. Topology based selection and curation of level sets. In H.-C. Hege, K. Polthier, and G. Scheuermann, editors, Topology-Based Methods in Visualization II, Mathematics and Visualization, pages 45-58. Springer Berlin Heidelberg, 2009.
5. L. Bavoil, M. Sainz, and R. Dimitrov. Image-space horizon-based ambient occlusion. In ACM SIGGRAPH 2008 talks, SIGGRAPH '08, New York, NY, USA, 2008. ACM.
6. K. Bidmon, S. Grottel, F. Bs, J. Pleiss, and T. Ertl. Visual abstractions of solvent pathlines near protein cavities. Computer Graphics Forum, 27(3):935-942, 2008.
7. D. Borland. Ambient occlusion opacity mapping for visualization of internal molecular structure. Journal of WSCG, 19(1):17-23, 2011.
8. M. P. Calace, T. Maiwald, and J. M. Thornton. PoreWalker: A novel tool for the identification and characterization of channels in transmembrane proteins from their three-dimensional structure. PLoS Computational Biology, 5(7), 2009.
9. M. Chavent, B. Lévy, and B. Maigret. High quality visualization of molecular skin surface. Journal of Molecular Graphics and Modelling, 27(2):1391-1398, 2008.
10. Y. Cho, D. Kim, H. Lee, J. Park, and D.-S. Kim. Reduction of the search space in the edge-tracing algorithm for the Voronoi diagram of 3d balls. In Computational Science and Its Applications-ICCSA 2006, volume 3980 of Lecture Notes in Computer Science, pages 111-120. Springer Berlin/Heidelberg, 2006. (Pubitemid 44058268)
11. R. G. Coleman and K. A. Sharp. Finding and characterizing tunnels in macromolecules with application to ion channels and pores. Biophys. J., 96:632-645, Oct. 2008.
12. J. Cortes, S. Barbe, M. Erard, and T. Simeon. Encoding molecular motions in voxel maps. IEEE/ACM Trans. Comput. Biol. Bioinformatics, 8:557-563, March 2011.
13. J. Cortes, T. Simon, V. R. de Angulo, D. Guieysse, M. Remaud-Simeon, and V. Tran. A path planning approach for computing large-amplitude motions of flexible molecules, 2005.
14. H. Edelsbrunner. Deformable smooth surface design. Discrete & Computational Geometry, 21(1):87-115, 1999.
15. H. Edelsbrunner and E. P.Mcke. Three-dimensional alpha shapes. ACM Trans. Graph., 13:43-72, January 1994.
16. T. Exner, M. Keil, G. Mckel, and J. Brickmann. Identification of substrate channels and protein cavities. Journal of Molecular Modeling, 4:340-343, 1998.
17. M. L. Gavrilova and J. Rokne. Updating the topology of the dynamic Voronoi diagram for spheres in euclidean d-dimensional space. Comput. Aided Geom. Des., 20:231-242, July 2003.
18. S. Hargreaves. Deferred shading. Game Developers Conference (GDC) talks, 2004.
19. B. K. Ho and F. Gruswitz. HOLLOW: Generating accurate representations of channel and interior surfaces in molecular structures. BMC structural biology, 8(1):49+, Nov. 2008.
20. C. Jones and K.-L. Ma. Visualizing flow trajectories using locality-based rendering and warped curve plots. IEEE Transactions on Visualization and Computer Graphics, 16:1587-1594, November 2010.
21. D.-S. Kim, Y. Cho, and D. Kim. Euclidean Voronoi diagram of 3d balls and its computation via tracing edges. Computer-Aided Design, 37(13):1412-1424, 2005. (Pubitemid 41042461)
22. D.-S. Kim, Y. Cho, and K. Sugihara. Quasi-worlds and quasi-operators on quasi-triangulations. Comput. Aided Des., 42:874-888, October 2010.
23. D.-S. Kim, D. Kim, Y. Cho, and K. Sugihara. Quasi-triangulation and interworld data structure in three dimensions. Computer-Aided Design, 38(7):808-819, 2006. (Pubitemid 44036794)
24. G. J. Kleywegt and T. A. Jones. Detection, delineation, measurement and display of cavities in macromolecular structures. Acta Crystallographica Section D, 50(2):178-185, Mar. 1994. (Pubitemid 2054290)
25. M. Krone, K. Bidmon, and T. Ertl. Interactive visualization of molecular surface dynamics. IEEE Transactions on Visualization and Computer Graphics, 15(6):1391-1398, 2009.
26. M. Krone, M. Falk, S. Rehm, J. Pleiss, and T. Ertl. Interactive exploration of protein cavities. To appear in Computer Graphics Forum (Proceedings of EG/IEEE EuroVis 2011), 2011.
27. S. Küchler, M. Radowski, T. Blaschke, M. Dathe, J. Plendl, R.Haag, M. Schäfer-Korting, and M. Kramer. Nanoparticles for skin penetration enhancement-A comparison of a dendritic coremultishell nanotransporter and solid lipid nanoparticles. Eur. J. Pharm. Biopharm., 71(2):243-250, 2009.
28. R. A. Laskowski. Surfnet: A program for visualizing molecular surfaces, cavities, and intermolecular interactions. Journal of Molecular Graphics, 13(5):323-330, 1995.
29. S. M. Lavalle. Rapidly-exploring random trees: A new tool for path planning, 1998.
30. J. Liang, H. Edelsbrunner, and C. Woodward. Anatomy of protein pockets and cavities: measurement of binding site geometry and implications for ligand design. Protein science: a publication of the Protein Society, 7(9):1884-1897, Sept. 1998. (Pubitemid 28432430)
31. N. Lindow, D. Baum, S. Prohaska, and H.-C. Hege. Accelerated visualization of dynamic molecular surfaces. Computer Graphics Forum, 29(3):943-952, 2010.
32. M. H. Maeda and K. Kinoshita. Development of new indices to evaluate protein-protein interfaces: Assembling space volume, assembling space distance, and global shape descriptor. Journal of Molecular Graphics and Modelling, 27(6):706-711, 2009.
33. M. Maňák, I. Kolingerová. Fast discovery of Voronoi vertices in the construction of Voronoi diagram of 3d balls. In Proceedings of the 2010 International Symposium on Voronoi Diagrams in Science and Engineering, ISVD '10, pages 95-104, Washington, DC, USA, 2010. IEEE Computer Society.
34. P. Medek, P. Beneš, and J. Sochor. Computation of tunnels in protein molecules using Delaunay triangulation. Journal of WSCG, University of West Bohemia, Pilsen, 15(1-3):107-114, 2007.
35. N. N. Medvedev, V. P. Voloshin, V. A. Luchnikov, and M. L. Gavrilova. An algorithm for three-dimensional Voronoi s-network. Journal of Computational Chemistry, pages 1676-1692, 2006. (Pubitemid 44476664)
36. A. Okabe, B. Boots, K. Sugihara, and S. N. Chiu. Spatial tessellations: Concepts and applications of Voronoi diagrams. Probability and Statistics. Wiley, NYC, 2nd edition, 2000. 671 pages.
37. Protein Data Bank. http://www.pdb.org.
38. M. Petrěk, P. Kosinová, J. Koca, and M. Otyepka. MOLE: A Voronoi diagram-based explorer of molecular channels, pores, and tunnels. Structure, 15(11):1357-1363, 2007. (Pubitemid 350051932)
39. M. Petrěk, M. Otyepka, P. Banas, P. Kosinová, J. Koca, and J. Damborsky. CAVER: a new tool to explore routes from protein clefts, pockets and cavities. BMC Bioinformatics, 7(1):316+, June 2006.
40. M. Raunest and C. Kandt. dxTuber: Detecting protein cavities, tunnels and clefts based on protein and solvent dynamics. Journal of Molecular Graphics and Modelling, 2010.
41. R. J. Rost. OpenGL(R) Shading Language (2nd Edition). Addison-Wesley Professional, January 2006.
42. T. Saito and T. Takahashi. Comprehensible rendering of 3-d shapes. volume 24, pages 197-206, New York, NY, USA, September 1990. ACM.
43. D. Siersma. Voronoi diagrams and Morse theory of the distance function. In Geometry in Present Day Science, World Scientific, pages 187-208. World Scientific, 1999.
44. C. Sigg, T. Weyrich, M. Botsch, and M. Gross. GPU-based ray-casting of quadratic surfaces. In Proceedings of the Eurographics Symposium on Point-Based Graphics, pages 59-65, 2006.
45. O. S. Smart, J. G. Neduvelil, X.Wang, B. A.Wallace, and M. S. Sansom. HOLE: a program for the analysis of the pore dimensions of ion channel structural models. Journal of Molecular Graphics, 14(6), Dec. 1996.
46. 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, 12:1237-1244, September 2006. (Pubitemid 44955660)
47. N. R. Voss and M. Gerstein. 3V: cavity, channel and cleft volume calculator and extractor. Nucleic Acids Research, 38(suppl 2):W555-W562, 2010.
48. E. Yaffe, D. Fishelovitch, H. J. Wolfson, D. Halperin, and R. Nussinov. MolAxis: Efficient and accurate identification of channels in macromolecules. Proteins: Structure, Function, and Bioinformatics, 73(1):72-86, 2008.
49. J. Yu, Y. Zhou, I. Tanaka, and M. Yao. Roll: a new algorithm for the detection of protein pockets and cavities with a rolling probe sphere. Bioinformatics, 26(1):46-52, Jan. 2010.