The Community for Technology Leaders
RSS Icon
Subscribe
Issue No.05 - September/October (1994 vol.14)
pp: 19-25
ABSTRACT
<p>We consider how we set out to formulate a parallel analytical molecular surface algorithm that has expected linear complexity with respect to the total number of atoms in a molecule. To achieve this goal, we avoided computing the complete 3D regular triangulation over the entire set of atoms, a process that takes time O(n log n), where n is the number of atoms in the molecule. We aim to compute and display these surfaces at interactive rates, by taking advantage of advances in computational geometry, making further algorithmic improvements and parallelizing the computations.</p>
CITATION
Amitabh Varshney, Frederick P. Brooks, Jr., William V. Wright, "Computing Smooth Molecular Surfaces", IEEE Computer Graphics and Applications, vol.14, no. 5, pp. 19-25, September/October 1994, doi:10.1109/38.310720
REFERENCES
1. F.M. Richards, "Areas, Volumes, Packing and Protein Structure,"Ann. Rev. Biophysics and Bioengineering, Vol. 6, 1977, pp. 151-176.
2. M.L. Connolly, "Analytical Molecular Surface Calculation,"J. Applied Crystallography, Vol. 16, No. 5, Oct. 1983, pp. 548-558.
3. G. Perrot et al., "MSEED: A Program for the Rapid Analytical Determination of Accessible Surface Areas and Their Derivatives,"J. Computational Chemistry, Vol. 13, No. 1, Jan./Feb. 1992, pp. 1-11.
4. H. Edelsbrunner, D. G. Kirkpatrick, and R. Seidel, "On the shape of a set of points in the plane,"IEEE Trans. Inform. Theory, vol. IT-29, no. 4, pp. 551-559, July 1983.
5. H. Edelsbrunner and E.P. Mücke, "Three-Dimensional Alpha Shapes,"ACM Trans. Graphics, Vol. 13, No. 1, Jan. 1994, pp. 43- 72.
6. H. Edelsbrunner, "Weighted Alpha Shapes," Tech. Report UIUCDCS-R-92-1760, Dept. of Computer Science, Univ. of Illinois at Urbana-Champaign, 1992.
7. F. Aurenhammer, "Power Diagrams: Properties, Algorithms and Applications,"SIAM J. Computing, Vol. 16, No. 1, Feb. 1987, pp. 78- 96.
8. R. Seidel, "Linear Programming and Convex Hulls Made Easy,"Sixth Ann. ACM Symp. on Computational Geometry, ACM Press, New York, 1990, pp. 211-215.
9. F. P. Preparata and M. I. Shamos,Computational Geometry, an Introduction. New York: Springer-Verlag, 1985.
10. I. Emiris and J. Canny, "An Efficient Approach to Removing Geometric Degeneracies," inEighth Ann. Symp. on Computational Geometry, ACM Press, New York, 1992, pp. 74-82.
11. A. Varshney, W.V. Wright, and F.P. Brooks, Jr., "Bounding the Number of Unit Spheres Inside a Larger Sphere," Tech. Report UNC-CS-TR-93.039, Dept. of Computer Science, Univ. of North Carolina at Chapel Hill, 1993.
12. R.E. Dickerson and I. Geis,The Structure and Action of Proteins, Harper&Row, New York, 1969.
13. S.J. Weiner et al., "A New Force Field for Molecular Mechanical Simulation of Nucleic Acids and Proteins,"J. Am. Chemical Soc., Vol. 106, No. 3, Feb. 1984, pp. 765-784.
14. H. Fuchs et al., "Pixel-Planes 5: A Heterogeneous Multiprocessor Graphics System Using Processor-Enhanced Memory,"Computer Graphics(Proc. Siggraph), Vol. 23, No. 3, July 1989, pp. 79-88.
30 ms
(Ver 2.0)

Marketing Automation Platform Marketing Automation Tool