]. R. References1, M. Abagyan, and . Totrov, Contact area dierence (cad): A robust measure to evaluate accuracy of protein models, J. Mol. Biol, vol.268, 1997.

S. Afraoui, F. Cazals, S. Loriot, P. Tuéry, and B. Villoutreix, A morphological study of pockets in protein-drugs complexes, 2007.

O. Aichholzer, F. Aurenhammer, T. Hackl, B. Jüttler, M. Oberneder et al., COMPUTATIONAL AND STRUCTURAL ADVANTAGES OF CIRCULAR BOUNDARY REPRESENTATION, Proc. 10th International Workshop on Algorithms and Data Structures (WADS), 2007.
DOI : 10.1142/S0218195911003548

M. V. Andrade and J. Stol, Exact algorithms for circles on the sphere, Internat. J. Comput. Geom. Appl, vol.11, p.267290, 2001.

K. Bastard, F. Cazals, C. Prevost, and S. Sachdeva, On the selection of best representative conformers, 2007.

J. L. Bentley and T. A. Ottmann, Algorithms for Reporting and Counting Geometric Intersections, IEEE Transactions on Computers, vol.28, issue.9, p.28643647, 1979.
DOI : 10.1109/TC.1979.1675432

E. Berberich, M. Hemmer, L. Kettner, E. Schömer, and N. Wolpert, An exact, complete and ecient implementation for computing planar maps of quadric intersection curves, Proceedings of the twenty-rst annual symposium on Computational geometry, p.99106, 2005.

E. Berberich, D. Fogel, R. Halperin, and . Wein, Sweeping and maintaining two-dimensional arrangements on surfaces, Proceedings of 23rd European Workshop on Computational Geometry, p.223226, 2007.
DOI : 10.1007/978-3-540-75520-3_57
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.106.9953

J. Boissonnat, P. Franco, and . Preparata, Robust Plane Sweep for Intersecting Segments, SIAM Journal on Computing, vol.29, issue.5, p.14011421, 2000.
DOI : 10.1137/S0097539797329373
URL : https://hal.archives-ouvertes.fr/inria-00073419

C. Burnikel, S. Funke, K. Mehlhorn, S. Schirra, and S. Schmitt, A separation bound for real algebraic expressions, Proc. 9th European Symposium on Algorithms, p.254265, 2001.
DOI : 10.1007/s00453-007-9132-4
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.20.7887

F. Cazals and S. Loriot, Computing the exact arrangement of circles on a sphere, with applications in structural biology, Proceedings of the twenty-third annual symposium on Computational geometry , SCG '07, 2006.
DOI : 10.1145/1247069.1247088
URL : https://hal.archives-ouvertes.fr/inria-00118781

F. Cazals, F. Proust, R. Bahadur, and J. Janin, Revisiting the voronoi description of protein-protein interfaces, Protein Science, vol.15, issue.9, p.20822092, 2006.
URL : https://hal.archives-ouvertes.fr/hal-00796062

. Cgal, Computational Geometry Algorithms Library

B. Chazelle, Application challenges to computational geometry: CG impact task force report, 1996.

B. Chazelle, Application challenges to computational geometry: CG impact task force report, Advances in Discrete and Computational Geometry, p.407463, 1999.
DOI : 10.1007/bfb0014485

C. Chotia and J. Janin, Principles of protein-protein recognition, Nature, vol.256, p.705708, 1975.

M. M. Pedro, S. De-castro, M. Pion, and . Teillaud, Exact and ecient computations on circles in CGAL Full version available as INRIA Research report No 6091, Exact and ecient computations on circles in CGAL and applications to VLSI design, Abstracts 23rd. European Workshop on Computational Geometry, p.219222, 2007.

O. Devillers, A. Fronville, B. Mourrain, and M. Teillaud, Algebraic methods and arithmetic ltering for exact predicates on circle arcs, Comput. Geom. Theory Appl, vol.22, p.119142, 2002.

S. Drysdale, G. Rote, and A. Sturm, Approximation of an open polygonal curve with a minimum number of circular arcs and biarcs, Proceedings of the 22nd European Workshop on Computational Geometry (EWCG), p.2528, 2006.
DOI : 10.1016/j.comgeo.2007.10.009

H. Edelsbrunner, M. Facello, and J. Liang, On the denition and the construction of pockets in macromolecules, Discrete Appl. Math, vol.88, p.83102, 1998.

H. Edelsbrunner and E. P. Mücke, Three-dimensional alpha shapes, ACM Trans. Graph, vol.13, issue.1, p.4372, 1994.
DOI : 10.1145/174462.156635
URL : http://arxiv.org/abs/math/9410208

Z. Ioannis, A. Emiris, S. Kakargias, M. Pion, E. P. Teillaud et al., Towards an open curved kernel, Proc. 20th Annu. ACM Sympos, p.438446, 2004.

. Exacus, Ecient and Exact Algorithms for Curves and Surfaces

A. Fabri and S. Pion, A generic lazy evaluation scheme for exact geometric computations, Proc. 2nd Library-Centric Software Design, 2006.
URL : https://hal.archives-ouvertes.fr/inria-00089229

E. Fogel and M. Teillaud, Generic programming and the CGAL library, Eective Computational Geometry for Curves and Surfaces, 2006.
URL : https://hal.archives-ouvertes.fr/hal-01053388

S. Funke and K. Mehlhorn, Look --- a Lazy Object-Oriented Kernel for geometric computation, Proceedings of the sixteenth annual symposium on Computational geometry , SCG '00, p.156165, 2000.
DOI : 10.1145/336154.336196

D. Gregor, J. Järvi, J. Siek, B. Stroustrup, G. D. Reis et al., Concepts: linguistic support for generic programming in C++, Proceedings of the 21st annual ACM SIGPLAN conference on Object-oriented programming languages, systems, and applications, p.291310, 2006.

S. Hert, M. Homann, L. Kettner, S. Pion, and M. Seel, An adaptable and extensible geometry kernel, Proc. Workshop on Algorithm Engineering, p.7990, 2001.
DOI : 10.1016/j.comgeo.2006.11.004
URL : https://hal.archives-ouvertes.fr/inria-00344964

G. Hummer, Hydrophobic force eld as a molecular alternative to surface-area models, J. Am. Chem. Soc, vol.121, p.62996305, 1999.

L. Kettner, K. Mehlhorn, S. Pion, S. Schirra, and C. Yap, Classroom examples of robustness problems in geometric computations, Proc. 12th European Symposium on Algorithms, p.702713, 2004.
URL : https://hal.archives-ouvertes.fr/inria-00344515

J. Keyser, T. Culver, D. Manocha, and S. Krishnan, MAPC, Proceedings of the fifteenth annual symposium on Computational geometry , SCG '99, p.360369, 1999.
DOI : 10.1145/304893.304990

C. Li and C. Yap, A new constructive root bound for algebraic expressions, Proc. 12th ACM-SIAM Symposium on Discrete Algorithms, p.496505, 2001.

C. Li, S. Pion, and C. Yap, Recent progress in exact geometric computation, The Journal of Logic and Algebraic Programming, vol.64, issue.1, p.85111, 2005.
DOI : 10.1016/j.jlap.2004.07.006
URL : https://hal.archives-ouvertes.fr/inria-00344355

B. Mourrain, J. Técourt, and M. Teillaud, On the computation of an arrangement of quadrics in 3D, Special issue, 19th European Workshop on Computational Geometry, p.145164, 2005.
DOI : 10.1016/j.comgeo.2004.05.003
URL : https://hal.archives-ouvertes.fr/inria-00350858

S. Pion and M. Teillaud, 2D circular kernel CGAL User and Reference Manual. 3.2 and 3.3 edition, p.2, 2006.

G. D. Rose, A. R. Geselowitz, G. J. Lesser, R. H. Lee, and M. H. Zehfus, Hydrophobicity of amino acid residues in globular proteins, Science, vol.229, issue.4716, p.8348, 1985.
DOI : 10.1126/science.4023714

R. Wein, B. Fogel, D. Zukerman, and . Halperin, 2D arrangements, CGAL User and Reference Manual, p.2

C. K. Yap and T. Dubé, THE EXACT COMPUTATION PARADIGM, Computing in Euclidean Geometry, p.452492, 1995.
DOI : 10.1142/9789812831699_0011

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