Visualization of Molecules with Positional Uncertainty

  • Penny Rheingans
  • Shrikant Joshi
Part of the Eurographics book series (EUROGRAPH)


Designing new and better chemotherapeutic compounds requires an understanding of the mechanism by which the drugs exert their biological effects. This involves consideration of the geometry of the active site, determination of the geometry of the drug, and analysis of the fit between them. This problem of drug-substrate fit, often called the docking problem, can be greatly influenced by uncertainty in the position of drug side chains. Traditional molecular graphics techniques fail to capture the distribution of likely atom positions. This paper describes a range of techniques for showing atom positions as probability distributions that more completely describe parameters which determine fit. ...


Geographic Information System Drug Molecule Iterate Function System Wire Frame Positional Uncertainty 
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.


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. 1.
    Kate Beard and William Mackaness: Visual Access to Data Quality in Geographic Information Systems. Cartographica, vol. 30, no. 2–3. (1993) 37–45CrossRefGoogle Scholar
  2. 2.
    Michael Burnett and Carroll Johnson: ORTEP-III: Oak Ridge Thermal Ellipsoid Plot Programs for Crystal Structure Illustrations. Oak Ridge National Laboratories Report ORNL-5138. (1996)Google Scholar
  3. 3.
    S. D. Goodsell, S. Mian, and A. J. Olson: Rendering volumetric data in molecular systems. Journal of Molecular Graphics, vol. 7. (1989) 41–47CrossRefGoogle Scholar
  4. 4.
    S. D. Goodsell: Visualizing Biological Molecules. Scientific American, vol. 267, no. 5. (1992)Google Scholar
  5. 5.
    Adrian Herzog: Modeling reliability on statistical surfaces by polygon filtering. In The Accuracy of Spatial Databases, Michael Goodchild and Sucharita Gopal, eds.. Taylor&Francis, London, (1989) 209–218Google Scholar
  6. 6.
    Suresh Lodha, Alex Pang, and Robert Sheehan, and Craig Wittenbrink: UFLOW: Visualizing Uncertainty in Fluid Flow. Proceedings of IEEE Visualization ‘86. IEEE Computer Society Press (1996) 249–254Google Scholar
  7. 7.
    Suresh Lodha, C.M. Wilson, and Robert Sheehan: LISTEN: sounding uncertainty visualization. Proceedings of IEEE Visualization ‘86. IEEE Computer Society Press, (1996) 189–196Google Scholar
  8. 8.
    W. E. Lorensen and H. E. Cline: Marching Cubes: A High Resolution 3D Surface Construction Algorithm. Computer Graphics, vol. 21. (1987) 163–169CrossRefGoogle Scholar
  9. 9.
    W. Schroeder. K. Martin.. and W. E. Lorensen: The Design and Implementation of an Object-oriented Toolkit for 3D Graphics and Visualization. Proceedings of IEEE Visualization ‘86 IEEE Computer Society Press. (1996) 93–100Google Scholar
  10. 10.
    David Theobald: Accuracy and bias in surface representation. In The Accuracy of Spatial Databases. Michael Goodchild and Sucharita Gopal, eds. Taylor&Francis, London, (1989) 99–106Google Scholar
  11. 11.
    R. M. Wadkins and D. E. Graves: Interactions of Anilinoacridines with Nucleic Acids: Effects of Substituent Modifications of DNA-Binding properties. Biochemistry, vol. 30, no. 17. (1991) 4277–4283CrossRefGoogle Scholar
  12. 12.
    Matthew Ward and Junwen Zheng: Visualization of Spatio-Temporal Data Quality. Proceedings of GIS/LIS ‘83. (1993) 727–737.Google Scholar
  13. 13.
    L. Westover: Footprint Evaluation for Volume Rendering. Computer Graphics, vol. 24. (1990) 367–376CrossRefGoogle Scholar
  14. 14.
    Craig Wittenbrink: IFS Fractal Interpolation of 2D and 3D Visualization. Proceedings of IEEE Visualization ‘85. IEEE Computer Society Press, (1995) 77–84Google Scholar

Copyright information

© Springer-Verlag/Wien 1999

Authors and Affiliations

  • Penny Rheingans
    • 1
  • Shrikant Joshi
    • 2
  1. 1.Department of Computer Science and Electrical EngineeringUniversity of Maryland. Baltimore CountyBaltimoreUSA
  2. 2.Celcore Inc.MemphisUSA

Personalised recommendations