Pocket Recognition on a Protein Using Euclidean Voronoi Diagram of Atoms

1. Angelov, B., Sadoc, J.-F., Jullien, R., Soyer, A., Mornon, J.-P., Chomilier, J.: Nonatomic solvent-driven Voronoi tessellation of proteins: an open tool to analyze protein folds. Proteins: Structure, Function, and Genetics 49, 446–456 (2002)

   Article  Google Scholar 

2. Connolly, M.L.: Solvent-accessible surfaces of proteins and nucleic acids. Science 221, 709–713 (1983)

   Article  Google Scholar 

3. Edelsbrunner, H., Facello, M., Liang, J.: On the definition and the construction of pockets in macromolecules. Discrete Applied Mathematics 88, 83–102 (1998)

   Article  MATH  MathSciNet  Google Scholar 

4. Gerstein, M., Tsai, J., Levitt, M.: The volume of atoms on the protein surface: calculated from simulation, using Voronoi polyhedra. Journal of Molecular Biology 249, 955–966 (1995)

   Article  Google Scholar 

5. Goede, A., Preissner, R., Frömmel, C.: Voronoi cell: new method for allocation of space among atoms: elimination of avoid- able errors in calculation of atomic volume and density. Journal of Computational Chemistry 18, 1113–1123 (1997)

   Google Scholar 

6. Kim, D.-S., Kim, D., Sugihara, K.: Voronoi diagram of a circle set from Voronoi diagram of a point set: I. Topology. Computer Aided Geometric Design 18, 541–562 (2001)

   Article  MATH  MathSciNet  Google Scholar 

7. Kim, D.-S., Kim, D., Sugihara, K.: Voronoi diagram of a circle set from Voronoi diagram of a point set: II. Geometry, Computer Aided Geometric Design 18, 563–585 (2001)

   Article  MATH  MathSciNet  Google Scholar 

8. Kim, D.-S., Cho, Y., Kim, D., Kim, S., Bhak, J.: Euclidean Voronoi Diagram of 3D Spheres and Applications to Protein Structure Analysis. In: International Symposium on Voronoi Diagrams in Science and Engineering, pp. 13–15. University of Tokyo, Tokyo (2004)

   Google Scholar 

9. Kim, D.-S., Cho, Y., Kim, D.: Edge-tracing algorithm for Euclidean Voronoi diagram of 3D spheres. In: Proc. 16th Canadian Conference on Computational Geometry, pp. 176–179 (2004)

   Google Scholar 

10. Kunts, I.D.: Structure-based strategies for drug design and discovery. Science 257, 1078–1082 (1992)

    Article  Google Scholar 

11. Lee, B., Richards, F.M.: The interpretation of protein structures: estimation of static accessibility. Journal of Molecular Biology 55, 379–400 (1971)

    Article  Google Scholar 

12. Liang, J., Edelsbrunner, H., Woodward, C.: Anatomy of protein pockets and cavities:Measurement of binding site geometry and implications for ligand design. Protein Science 7, 1884–1897 (1998)

    Article  Google Scholar 

13. Parsons, D., Canny, J.: Geometric problems in molecular biology and robotics. In: 2nd International Conference on Intelligent Systems for Molecular Biology, Palo Alto, CA, pp. 322–330 (1994)

    Google Scholar 

14. Peters, K.P., Fauck, J., Frömmel, C.: The Automatic Search for Ligand Bind¬ing Sites in Protein of Know Three-dimensional Strucutre Using only Geometric Criteria. Journal of Molecular Biology 256, 201–213 (1996)

    Google Scholar 

15. RCSB Protein Data Bank (2004), http://www.rcsb.org/pdb/

16. Zimmer, R., Wöhler, M., Thiele, R.: New scoring schemes for protein fold recognition based on Voronoi contacts. Bioinformatics 14, 295–308 (1998)

    Google Scholar 

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