Real-time triangulation of molecular surfaces

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

Volumn 4705 LNCS, Issue PART 1, 2007, Pages 55-67

  Ryu, Joonghyun ^a   Park, Rhohun ^a   Seo, Jeongyeon ^a   Kim, Chongmin ^a   Lee, Hyun Chan ^b   Kim, Deok Soo ^a  

^a Hanyang University   (South Korea)

^b Hong Ik University   (South Korea)

Author keywords

A molecular surface; A protein; A voronoi diagram of atoms; Shape

Indexed keywords

ALGORITHMS; MOLECULAR STRUCTURE; REAL TIME SYSTEMS;

MOLECULAR SURFACE; VORONOI DIAGRAM OF ATOMS;

PROTEINS;

EID: 38049015362     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-540-74472-6_5     Document Type: Conference Paper

References (27)

1. Lee, B., Richards, F.M.: The interpretation of protein structures: Estimation of static accessibility. Journal of Molecular Biology 55, 379-400 (1971)
2. Richards, F.M.: Areas, volumes, packing, and protein structure. Annual Review of Biophysics and Bioengineering 6, 151-176 (1977)
3. Connolly, M.L.: Solvent-accessible surfaces of proteins and nucleic acids. Science 221, 709-713 (1983)
4. Connolly, M.L.: Molecular surfaces: A review. Network Science (1996), http://www.netsci.org/Science/Compchem/feature14.html
5. Leach, A.R.: Molecular Modelling: Principles and Applications. Prentice-Hall, Englewood Cliffs (2001)
6. Bourne, P.E., Addess, K.J., Bluhm, W.F., Chen, L., Deshpande, N., Feng, Z., Fleri, W., Green, R., Merino-Ott, J.C., Townsend-Merino, W., Weissig, H., Westbrook, J., Berman, H.M.: The distribution and query systems of the rcsb protein data bank. Nucleic Acids Research 32, D223-D225 (2004)
7. Connolly, M.L.: Molecular surface triangulation. Journal of Applied Crystallography 18, 499-505 (1985)
8. Ryu, J., Park, R., Kim, D.S.: Molecular surfaces on proteins via beta shapes. Computer-Aided Design (2007) (in press)
9. Ryu, J., Park, R., Clio, Y., Seo, J., Kim, D.S.: beta-shape based computation of blending surfaces on a molecule. In: The 4th ISVD International Symposium on Voronoi Diagrams in Science and Engineering (2007) (accepted)
10. Connolly, M.L.: Analytical molecular surface calculation. Journal of Applied Crystallography 16, 548-558 (1983)
11. Sanner, M., Olson, A.J., Spehner, J.-C.: Reduced surface: An efficient way to compute molecular surfaces. Biopolymers 38, 305-320 (1996)
12. Varshney, A., Brooks, Jr., W.V.W.: Computing smooth molecular surfaces. IEEE Computer Graphics and Applications 14, 19-25 (1994)
13. Bajaj, C.L., Lee, H.Y., Merkert, R., Pascucci, V.: NURBS based b-rep models for macromolecules and their properties. In: Proceedings of the 4th Symposium on Solid Modeling and Applications, pp. 217-228 (1997)
14. Bajaj, C.L., Pascucci, V., Shamir, A., Holt, R.J., Netravali, A.N.: Dynamic maintenance and visualization of molecular surfaces. Discrete Applied Mathematics 127(1), 23-51 (2003)
15. Edelsbrunner, H.: Deformable smooth surface design. Discrete & Computational Geometry 21, 87-115 (1999)
16. Cheng, H.L., Dey, T.K., Edelsbrunner, H., Sullivan, J.M.: Dynamic skin triangulation. Discrete & Computational Geometry 25(4), 525-568 (2001)
17. Cheng, H.-L., Shi, X.: Guaranteed quality triangulation of molecular skin surfaces. In: [Vis 2004] IEEE Visualization, Austin, Texas, USA, October 10-15, pp. 481-488. IEEE Computer Society Press, Los Alamitos (2004)
18. Kim, D.S., Cho, Y., Kim, D.: Euclidean Voronoi diagram of 3D balls and its computation via tracing edges. Computer-Aided Design 37(13), 1412-1424 (2005)
19. Kim, D., Kim, D.S.: Region-expansion for the Voronoi diagram of 3D spheres. Computer-Aided Design 38(5), 417-430 (2006)
20. Kim, D.S., Kim, D., Cho, Y., Sugihara, K.: Quasi-triangulation and interworld data struction in three dimensions. Computer-Aided Design 38(7), 808-819 (2006)
21. Edelsbrunner, H., Kirkpatrick, D.G., Seidel, R.: On the shape of a set of points in the plane. IEEE Transactions on Information Theory IT-29(4), 551-559 (1983)
22. Edelsbrunner, H., Mücke, E.P.: Three-dimensional alpha shapes. ACM Transactions on Graphics 13(1), 43-72 (1994)
23. Edelsbrunner, H.: The union of balls and its dual shape. Discrete & Computational Geometry 13, 415-440 (1995)
24. Halperin, D., Overmars, M.H.: Spheres, molecules, and hidden surface removal. In: Proceedings of the 10th ACM Symposium on Computational Geometry, pp. 113-122. ACM Press, New York (1994)
25. Berman, H., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T., Weissig, H., Shindyalolv, I., Bourne, P.: The protein data bank. Nucleic Acids Research 28, 235-242 (2000)
26. RCSB: Protein Data Bank Homepage, http://www.rcsb.org/pdb/
27. Seidl, T., Kriegel, H.-P.: Solvent accessible surface representation in a database system for protein docking. In: ISMB'95. Proceedings of the 3rd International Conference on Intelligent Systems for Molecular Biology, pp. 350-358. AAAI Press, USA (1995)