Connolly surface on an atomic structure via Voronoi diagram of atoms

Journal of Computer Science and Technology

Volumn 21, Issue 2, 2006, Pages 255-260

  Ryu, Joonghyun ^a   Park, Rhohun ^a   Kim, Deok Soo ^a,b  

^a Hanyang University   (South Korea)

^b Voronoi Diagram Research Center   (South Korea)

Author keywords

shape; Blending surface; Connolly molecular surface; Protein; Voronoi diagram of atoms

Indexed keywords

Β-SHAPE; BLENDING SURFACE; CONNOLLY/MOLECULAR SURFACE; VORONOI DIAGRAM OF ATOMS;

ALGORITHMS; COMPUTER GRAPHICS; GEOMETRY; PROTEINS;

CRYSTAL ATOMIC STRUCTURE;

EID: 33645944988     PISSN: 10009000     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11390-006-0255-x     Document Type: Article

References (16)

1. Connolly M L. Solvent-accessible surfaces of proteins and nucleic acids. Science, 1983, 221: 709-713.
2. Connolly M L. Analytical molecular surface calculation. Journal of Applied Crystallography, 1983, 16: 548-558.
3. Richards F M. Areas, volumes, packing and protein structure. Annu. Rev. Biophys. Bioeng., 1977, 6: 151-176.
4. Varshney A, Brooks F P Jr, Richardson D C. Defining, computing, and visualizing molecular interfaces. In Proc. 6th IEEE Visualization Conference, Atlanta, USA, Oct. 1995, pp.36-43.
5. Halperin I, Ma B, Wolfson H, Nussinov R. Principles of docking: An overview of search algorithms and a guide to scoring functions. PROTEINS: Structure, Function, and Genetics, 2002, 47: 409-443.
6. Lee B, Richards F M. The interpretation of protein structures: Estimation of static accessibility. Journal of Molecular Biology, 1971, 55: 379-400.
7. Sanner M F, Olson A J, Spehner J-C. Reduced surface: An efficient way to compute molecular surfaces. Biopolymers, 1996, 38(3): 305-320.
8. Halperin D, Overmars M H. Spheres, molecules, and hidden surface removal. In Proc. 10th ACM Symp. Computational Geometry, Stony Brook, NY, USA, June 1994, pp.113-122.
9. Varshney A, Brooks F P Jr, Wright W V. Computing smooth molecular surfaces. IEEE Computer Graphics and Applications, 1994, 14(5): 19-25.
10. Bajaj C L, Lee H Y, Merkert R, Pascucci V. NURBS based B-rep models for macromolecules and their properties. In Proc. 4th Symposium on Solid Modeling and Applications, Atlanta, USA, May 1997, pp.217-228.
11. Bajaj C L, Pascucci V, Shamir A, Holt R J, Netravali A N. Dynamic maintenance and visualization of molecular surfaces. Discrete Applied Mathematics, 2003, 127: 23-51.
12. Kim D-S, Cho Y, Kim D et al. Euclidean Voronoi diagram of 3D spheres and applications to protein structure analysis. In Proc. Int. Symp. Voronoi Diagrams in Science and Engineering, Tokyo, 2004, pp.137-144.
13. Kim D-S, Cho Y, Kim D. Euclidean Voronoi diagram of 3D balls and its computation via tracing edges. Computer-Aided Design, 2005, 37(13): 1412-1424.
14. Kim D-S, Cho C-H, Kim D, Cho Y. Recognition of docking sites on a protein using β-shape based on Voronoi diagram of atoms. Computer-Aided Design, (to appear)
15. Edelsbrunner H, Mücke E P. Three-dimensional alpha shapes. ACM Trans. Graphics, 1994, 13(1): 43-72.
16. Kim D-S, Cho C-H, Ryu J, Kim D. Three dimensional beta shapes, (submitted to Computer-Aided Design)