Computing the arrangement of circles on a sphere, with applications in structural biology

Computational Geometry: Theory and Applications

Volumn 42, Issue 6-7, 2009, Pages 551-565

  Cazals, Frédéric ^a   Loriot, Sébastien ^a,b  

^a INRIA   (France)

^b UNIVERSITÉ DE BOURGOGNE   (France)

Author keywords

Arrangement of circles; Docking; Spheres; Van der Waals models

Indexed keywords

EID: 84867973317     PISSN: 09257721     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.comgeo.2008.10.004     Document Type: Article

References (30)

1. P. Agarwal, L. Guibas, A. Nguyen, D. Russel, and L. Zhang Collision detection for deforming necklaces Computational Geometry: Theory and Applications 28 2004 137 163
2. N. Akkiraju, and H. Edelsbrunner Triangulating the surface of a molecule Discrete Applied Mathematics 71 1996 5 22
3. N. Alon, H. Last, R. Pinchasi, and M. Sharir On the complexity of arrangements of circles in the plane Discrete and Computational Geometry 26 4 2001 465 492
4. N. Amenta, S. Choi, and R.K. Kolluri The power crust, unions of balls, and the medial axis transform Computational Geometry: Theory and Applications 19 2 2001 127 153
5. J.L. Bentley, and T.A. Ottmann Algorithms for reporting and counting geometric intersections IEEE Transactions on Computers 28 9 1979 643 647
6. J.-D. Boissonnat, and M. Yvinec Algorithmic Geometry 1998 Cambridge University Press UK translated by Hervé Brönnimann
7. P.M.M. de Castro, F. Cazals, S. Loriot, and M. Teillaud Design of the CGAL 3D Spherical Kernel and application to arrangements of circles on a sphere Computational Geometry: Theory and Applications 42 6-7 2009 536 550 this issue
8. F. Cazals, and S. Loriot Computing the exact arrangement of circles on a sphere, with applications in structural biology Research Report 6049, INRIA, 2006 https://hal.inria.fr/inria-00118781
9. F. Chazal, D. Cohen-Steiner, and Q. Mérigot Stability of boundary measure Research Report 6219, INRIA, 2007 http://hal.inria.fr/inria-00154798
10. M.L. Connolly Molecular surfaces: A review Network Science 14 1996 http://www.netsci.org/Science/Compchem/feature14.html
11. M. de Berg, M. van Kreveld, M. Overmars, and O. Schwarzkopf Computational Geometry: Algorithms and Applications 1997 Springer-Verlag Berlin
12. E. Eyal, D. Halperin, Dynamic maintenance of molecular surfaces under conformational changes, in: Proc. 21st Annual Symposium on Computational Geometry, 2005, pp. 45-54
13. U. Feige A threshold of ln n for approximating set cover Journal of the ACM (JACM) 45 4 1998 634 652
14. M.R. Garey, and D.S. Johnson Computers and Intractability: A Guide to the Theory of NP-Completeness 1979 W.H. Freeman New York
15. A. Gordon Classification 1999 Chapman & Hall/CRC
16. D. Halperin, and C.R. Shelton A perturbation scheme for spherical arrangements with application to molecular modeling Computational Geometry: Theory and Applications 10 4 1998 273 288
17. J. Janin, and S. Wodak The Third CAPRI Assessment Meeting Toronto, Canada, April 20-21, 2007 Structure 15 7 2007 755 759
18. L. Kettner, Halfedge data structures, in: C.E. Board (Ed.), CGAL User and Reference Manual, 3.3 edition, 2007
19. P. Koehl Electrostatics calculations: Latest methodological advances Current Opinion in Structural Biology 16 2 2006 142 151
20. M. Lensink, R. Mendez, and S. Wodak Docking and scoring protein complexes: CAPRI 3rd edition Proteins 69 4 2007 704 718
21. N. London, and O. Schueler-Furman Funnel hunting in a rough terrain: Learning and discriminating native energy funnels Structure 16 2 2008 269 279
22. S. Loriot, S. Sachdeva, K. Bastard, C. Prevost, and F. Cazals On the characterization and selection of diverse conformational ensembles Research Report 6503, INRIA, 04 2008 https://hal.inria.fr/inria-00252046
23. J. Monod, J. Wyman, and J.-P. Changeux On the nature of allosteric transitions: A plausible model Journal of Molecular Biology 12 1965 88 118
24. S. Rusinkiewicz, M. Levoy, QSplat: A multiresolution point rendering system for large meshes, in: Proc. 27th Annual Conference on Computer Graphics and Interactive Techniques (SIGGRAPH), 2000, pp. 343-352
25. B.K. Shoichet, D.L. Bodian, and I.D. Kuntz Molecular docking using shape descriptors Journal of Computational Chemistry 13 3 1992 380 397
26. C.M. Summa, M. Levitt, and W.F. DeGrado An atomic environment potential for use in protein structure prediction Journal of Molecular Biology 352 4 2005 986 1001
27. R.E. Tarjan Data Structures and Network Algorithms CBMS-NSF Regional Conference Series in Applied Mathematics vol. 44 1983 Society for Industrial and Applied Mathematics Philadelphia, PA
28. R. Wein, E. Fogel, B. Zukerman, and D. Halperin Advanced programming techniques applied to CGAL's arrangement package Computational Geometry: Theory and Applications 38 1-2 2007 37 63
29. Z. Xiang, C.S. Soto, and B. Honig Evaluating conformational free energies: The colony energy and its application to the problem of loop prediction Proceedings of the National Academy of Sciences 99 11 2002 7432 7437
30. M. Zacharias Protein-protein docking with a reduced protein model accounting for side-chain flexibility Protein Science 12 6 2003 1271 1282