Fast and efficient computation of additively weighted voronoi cells for applications in molecular biology

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 1432, Issue , 1998, Pages 310-321

  Will, Hans Martin ^a  

^a ETH ZURICH   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHMS; BIOLOGY; BIOMOLECULES; BIOPHYSICS; CELLS; CYTOLOGY; MOLECULAR BIOLOGY;

EFFICIENT COMPUTATION; EXPECTED TIME; PROBLEM INSTANCES; RANDOMIZED ALGORITHMS; UPPER BOUND; VORONOI CELL;

COMPUTATIONAL EFFICIENCY;

EID: 84957665294     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/BFb0054378     Document Type: Conference Paper

References (27)

1. Andrade, M. V., & Stolfi, J. (1998). Exact Algorithms for Circles on the Sphere. To appear in Proc. 14th Annu. ACM Sympos. Comput. Geom.
2. Aurenhammer, F. (1987). Power diagrams: properties, algorithms and applications. SIAM J. Comput., 16, 78-96.
3. Aurenhammer, F. (1991). Voronoi diagrams: A survey of a fundamental geometric data structure. ACM Comput. Surv., 23, 345-405.
4. de Berg, M., Dobrindt, K., & Schwarzkopf, O. (1995). On lazy randomized incremental construction. Discrete Comput. Geom., 14, 261-286.
5. Boissonnat, J. D., & Dobrindt, K. T. G. (1996). On-line construction of the upper envelope of triangles and surface patches in three dimensions. Comput. Geom. Theory Appl., 5, 303-320.
6. Chazelle, B. (1993). An optimal convex hull algorithm in any fixed dimension. Discrete Comput. Geom., 10, 377-409.
7. Clarkson, K. L., & Shor, P. W. (1989). Applications of random sampling in computational geometry, II, Discrete Comput. Geom., 4, 387-421.
8. Gerstein, M., Tsal, J., & Levitt, M. (1995). The Volume of Atoms on the Protein Surface: Calculated from Simulation, using Voronoi Polyhedra. Journal of Molecular Biology, 249, 955-966.
9. Geysen, H. M., Talner, J. A., Rodda, S. J., Mason, T. J., Alexander, H., Getzoff, E. D., & Lerner, R. A. (1987). Chemistry of antibody binding to a protein. Science, 235, 1184-1190.
10. Goede, A., Preißner, R., & Frömmel, C. (1997). Voronoi Cell-A new method for the allocation of space among atoms. Journal of Computational Chemistry.
11. Gschwend, D. A. (1995). Dock, version 3.5. San Francisco: Department of Pharmaceutical Chemistry, University of California.
12. Guibas, L. J., & Sedgewick, R. (1978). A diochromatic framework for balanced trees. Proc. 19th Annu. Sympos. Foundations of Computer Science. (pp. 8-21).
13. Halperin, D., & Shehon, C. (1997). A perturbation scheme for spherical arrangements with application to molecular modeling, Proc. 13th Annu. ACM Sympos. Comput. Geom. (pp. 183-192).
14. Kirkpatrick, D. G. (1983). Optimal search in planar subdivisions. SIAM J. Cornput., 12, 28-35.
15. Kleywegt, G. T., & Jones, T. A. (1994). Detection, delineation, measurement and display of cavities in macromolecular structures. Acta CrystaUographica, D50, 178-185.
16. Kyte, J. (1995). Structure in Protein Chemistry. Garland Publishing.
17. Lawson, C. L. (1977). Software for C1 surface interpolation. In J. R. Rice (Ed.), Math. Software III (pp. 161-194). New York, NY: Academic Press.
18. Meijering, J. L. (1953). Interface area, edge length, and number of vertices in crystal aggregates with random nucleation: Philips Research Report.
19. Moller, J. (1992). Random Johnson-Mehl tesselations. Adv. Appl. Prob., 24, 814-844.
20. Mulmuley, K. (1994). An Efficient Algorithm for Hidden Surface Removal, II. Journal of Computer and Systems Sciences, 49, 427-453.
21. Okabe, A., Boots, B., & Sugihara, K. (1992). Spatial Tessellations: Concepts and Applications of Voronoi Diagrams. Chichester, UK: John Wiley & Sons.
22. Pontius, J., Richelle, J., & Wodak, S. J. (1996). Deviations from Standard Atomic Volumes as a Quality Measure for Protein Crystal Structures. Journal of Molecular Biology, 264, 121-136.
23. Preparata, F. P., & Hong, S. J. (1977). Convex hulls of finite point sets in two and three dimensions. Comm. ACM 20, (pp. 87-93)
24. Ruppert, J. (1993). A New and Simple Algorithm for Quality 2-Dimensional Mesh Generation, Proc. 4th ACM-SIAM Sympos. Discrete Algorithms (pp. 83-92).
25. Seidel, R. (1993). Backwards analysis of randomized geometric algorithms. In J. Pach (Ed.), New Trends in Discrete and Computational Geometry, (pp. 37-67). Berlin: Springer-Verlag
26. Tilton, R. F., Singh, U. C., Weiner, S. J., Connolly, M. L., Kuntz, I. D., Kollman, P. A., Max, N., & Case, D. A. (1986). Computational Studies of the interaction of myoglobin and xenon. Journal of Molecular Biology, 192, 443-456.
27. Yeates, T. O. (1995). Algorithms for evaluating the long range accessability of protein surfaces. Journal of Molecular Biology, 249(4), 804-815.