Advertisement

Direct Volume Rendering of Volumetric Protein Data

  • Min Hu
  • Wei Chen
  • Tao Zhang
  • Qunsheng Peng
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4035)

Abstract

The visualization of 3D volume data of proteins synthesized by quantum mechanics is a new topic and is of great importance in modern bio-computing. In this paper, we introduce our primary attempts on the volume visualization of the 3D macro-molecular scalar field. Firstly, we transform one protein molecular structure into a regularly sampled 3D scalar field according to the theories in quantum chemistry, in which each node records the combined effect of different actions in protease. We then exploit volume rendering techniques to find the macro-structure inside the data field based on a convenient mapping mechanism. We also propose an improved transfer function mode, facilitating the flexible visualization of the 3D protein data sets. Finally, combined with the iso-surface extraction technique, our approach allows for interactive exploration of the potential “tunnel” region which exhibits biological sense. With our approach, we show the escape route of water molecules hidden in the HIV-1 protease, which conforms to the experimental results.

Keywords

Transfer Function Nodal Surface Direct Volume Volume Visualization IEEE Visualization 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    Leach, A.R.: Molecular Modelling Principles and Applications. Prentice-Hall, Englewood Cliffs (2001)Google Scholar
  2. 2.
    Bajaj, C., Pascucci, V., Schikore, D.: The Contour Spectrum. In: Proceedings of the 1997 IEEE Visualization Conference, pp. 167–173.Google Scholar
  3. 3.
    Johnson, C.: Top Scientific Visualization Research Problems. IEEE Computer Graphics and Applications 24(4), 13–17 (2004)CrossRefGoogle Scholar
  4. 4.
    Stan, C., Tsai: An introduction to computational biochemistry. Wiley-Liss, Inc., New York (2002)Google Scholar
  5. 5.
    Hoenigmann, D., Ruisz, J., Haider, C.: Adaptive Design of a Global Opacity Transfer Function for Direct Volume Rendering of Ultrasound Data. In: IEEE Visualization 2003, Seattle, Washington, USA, pp. 489–496 (2003)Google Scholar
  6. 6.
    Kindlmann, G., Whitaker, R., Tasdizen, T., Moeller, T.: Curvature-Based Transfer Functions for Direct Volume Rendering: Methods and Applications. In: IEEE Visualization 2003, Seattle, Washington, USA, pp. 513–520 (2003)Google Scholar
  7. 7.
    Kindlmann, G., Durkin, J.W.: Semi-Automatic Generation of Transfer Functions for Direct Volume Rendering. In: Proceedings of the 1998 Symposium on Volume visualization, pp. 79–86 (1998)Google Scholar
  8. 8.
    Gerig, G., Kindlemann, G., et al.: Image Processing for Volume Graphics. In: A Course for SIGGRAPH 2002 (2002)Google Scholar
  9. 9.
    Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindya-lov, I.N., Bourne, P.E.: The Protein Data Bank. Nucleic Acids Research 28, 235–242 (2000)CrossRefGoogle Scholar
  10. 10.
    Pfister, H., Lorensen, B., Bajaj, C., Kindlmann, G.: The Transfer Function Bake-Off. IEEE Computer Graphics and Applications 21(3), 16–22 (2001)CrossRefGoogle Scholar
  11. 11.
    Levine, I.N.: Quantum Chemistry. Prentice-Hall, Englewood Cliffs (2004)Google Scholar
  12. 12.
    Kniss, J., Kindlmann, G., Hansen, C.: Multidimensional Transfer Functions for Interactive Volume Rendering. IEEE Transactions on Visualization and Computer Graphics 8(3), 270–285 (2002)CrossRefGoogle Scholar
  13. 13.
    Kniss, J., Premǒze, S., Ikits, M., Lefohn, A., et al.: Gaussian Transfer Functions for Multi-Field Volume Visualization. In: IEEE Visualization 2003, Seattle, Washington, USA, pp. 497–504 (2003)Google Scholar
  14. 14.
    Engel, K., Kraus, M., Ertl, T.: High-Quality Pre-Integrated Volume Rendering Using Hard-ware-Accelerated Pixel Shading. In: Eurographics/SIGGRAPH Workshop on Graphics Hardware (2001)Google Scholar
  15. 15.
    Kniss, J.M., Van Uitert, R., Stephens, A., Li, G.-S., Tasdizen, T.: Statistically Quantitative Volume Visualization. In: IEEE Visualization 2005, Minneapolis, USA, pp. 287–294 (2005)Google Scholar
  16. 16.
    Levoy, M.: Display of Surfaces from Volume Data. IEEE CG & A 8(5), 29–37 (1988)Google Scholar
  17. 17.
    Nicoletti, G.M.: Volume visualization: advances in transfer and opacity function generation for interactive direct volume rendering. In: Proceedings of the Thirty-Sixth Southeastern Symposium on System Theory, pp. 1–5 (2004)Google Scholar
  18. 18.
    Mehta, S., Hazzard, K., Machiraju, R.: Detection and Visualization of Anomalous Structures in Molecular Dynamics Simulation Data. In: IEEE Visualization 2004, Texas, USA, pp. 465–472 (2004)Google Scholar
  19. 19.
    Takahashi, S., Takeshima, Y., Fujishiro, I.: Topological volume skeletonization and its application to transfer function design. Graphical Models 66, 24–49 (2004)MATHCrossRefGoogle Scholar
  20. 20.
    Potts, S., Möller, T.: Transfer Functions on a Logarithmic Scale for Volume Rendering. In: Proceedings of Graphics Interfaces 2004, London, Ontario, pp. 57–63 (May 2004)Google Scholar
  21. 21.
    Elvins, T.T.: A Survey of Algorithms for Volume Visualization. Computer Graphics 26(3), 194–201 (1992)CrossRefGoogle Scholar
  22. 22.
    Qiao, W., Ebert, D.S., Entezari, A., Korkusinski, M., Klimeck, G.: VolQD: Direct Volume Rendering of Multi-million Atom Quantum Dot Simulations. In: IEEE Visualization 2005, Inneapolis, MN, USA, pp. 319–326 (October 2005)Google Scholar
  23. 23.
    Humphrey, W., Dalke, A., Schulten, K.: VMD - Visual Molecular Dynamics. Journal of Molecular Graphics 14(1), 33–38 (1996)CrossRefGoogle Scholar
  24. 24.
    Tao, W.: Personal CommunicationGoogle Scholar
  25. 25.
    http://molvis.sdsc.edu/protexpl/frntdoor.htm (Last visiting data: 2006-1-12)
  26. 26.
    http://www.rasmol.org/ (Last visiting data: 2006-1-12)

Copyright information

© Springer-Verlag Berlin Heidelberg 2006

Authors and Affiliations

  • Min Hu
    • 1
  • Wei Chen
    • 1
  • Tao Zhang
    • 1
  • Qunsheng Peng
    • 1
  1. 1.State Key Lab of CAD & CGZhejiang UniversityHangzhouChina

Personalised recommendations