P. Agarwal, L. Guibas, A. Nguyen, D. , and L. Zhang, Collision detection for deforming necklaces, Computational Geometry, vol.28, issue.2-3, pp.137-163, 2004.
DOI : 10.1016/j.comgeo.2004.03.008

N. Akkiraju and H. Edelsbrunner, Triangulating the surface of a molecule, Discrete Applied Mathematics, vol.71, issue.1-3, pp.5-22, 1996.
DOI : 10.1016/S0166-218X(96)00054-6

N. Alon, H. Last, R. Pinchasi, and M. Sharir, On the Complexity of Arrangements of Circles in the Plane, Discrete & Computational Geometry, vol.26, issue.4, pp.465-492, 2001.
DOI : 10.1007/s00454-001-0043-x

N. Amenta, S. Choi, and R. K. Kolluri, The power crust, unions of balls, and the medial axis transform, Computational Geometry, vol.19, issue.2-3, pp.127-153, 2001.
DOI : 10.1016/S0925-7721(01)00017-7

J. L. Bentley and T. A. Ottmann, Algorithms for Reporting and Counting Geometric Intersections, IEEE Transactions on Computers, vol.28, issue.9, pp.643-647, 1979.
DOI : 10.1109/TC.1979.1675432

URL : http://www.dtic.mil/get-tr-doc/pdf?AD=ADA058768

J. Boissonnat and M. Yvinec, Algorithmic Geometry, 1998.
DOI : 10.1017/CBO9781139172998

P. 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, vol.42, issue.6-7
DOI : 10.1016/j.comgeo.2008.10.003

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. Chazal, D. Cohen-steiner, and Q. Mérigot, Stability of boundary measure, Research Report, vol.6219, 2007.

M. L. Connolly, Molecular surfaces: a review, Network Science, vol.14, 1996.

M. De-berg, M. Van-kreveld, M. Overmars, and O. Schwarzkopf, Computational Geometry: Algorithms and Applications, 1997.

E. Eyal and D. Halperin, Dynamic maintenance of molecular surfaces under conformational changes, Proceedings of the twenty-first annual symposium on Computational geometry , SCG '05, pp.45-54, 2005.
DOI : 10.1145/1064092.1064102

U. Feige, A threshold of ln n for approximating set cover, Journal of the ACM, vol.45, issue.4, pp.634-652, 1998.
DOI : 10.1145/285055.285059

M. R. Garey and D. S. Johnson, Computers and Intractability: A Guide to the Theory of NP- Completeness, 1979.

D. Halperin and C. R. Shelton, A perturbation scheme for spherical arrangements with application to molecular modeling, Computational Geometry, vol.10, issue.4, pp.273-288, 1998.
DOI : 10.1016/S0925-7721(98)00014-5

J. Janin and S. Wodak, The Third CAPRI Assessment Meeting Toronto,??Canada, April 20???21, 2007, Structure, vol.15, issue.7, pp.755-759, 2007.
DOI : 10.1016/j.str.2007.06.007

L. Kettner, Halfedge data structures, CGAL User and Reference Manual. 3.3 edition, 2007.

M. Lensink, R. Mendez, and S. Wodak, Docking and scoring protein complexes: CAPRI 3rd Edition, Proteins: Structure, Function, and Bioinformatics, vol.15, issue.Suppl 7, pp.704-722, 2007.
DOI : 10.1002/prot.21804

N. London and O. Schueler-furman, Funnel Hunting in a Rough Terrain: Learning and Discriminating Native Energy Funnels, Structure, vol.16, issue.2, pp.269-279, 2008.
DOI : 10.1016/j.str.2007.11.013

S. Loriot, S. Sachdeva, K. Bastard, C. Prevost, and F. Cazals, On the characterization and selection of diverse conformational ensembles, Research Report, vol.6503, 2008.
URL : https://hal.archives-ouvertes.fr/inria-00252046

J. Monod, J. Wyman, and J. Changeux, On the nature of allosteric transitions: A plausible model, Journal of Molecular Biology, vol.12, issue.1, pp.88-118, 1965.
DOI : 10.1016/S0022-2836(65)80285-6

S. Rusinkiewicz and M. Levoy, QSplat, Proceedings of the 27th annual conference on Computer graphics and interactive techniques , SIGGRAPH '00, pp.343-352, 2000.
DOI : 10.1145/344779.344940

B. K. Shoichet, D. L. Bodian, and I. D. Kuntz, Molecular docking using shape descriptors, Journal of Computational Chemistry, vol.103, issue.3, pp.380-397, 1992.
DOI : 10.1002/jcc.540130311

C. M. Summa, M. Levitt, and W. F. Degrado, An Atomic Environment Potential for use in Protein Structure Prediction, Journal of Molecular Biology, vol.352, issue.4, pp.986-1001, 2005.
DOI : 10.1016/j.jmb.2005.07.054

R. E. Tarjan, Data Structures and Network Algorithms, CBMS-NSF Regional Conference Series in Applied Mathematics. Society for Industrial and Applied Mathematics, vol.44, 1983.
DOI : 10.1137/1.9781611970265

R. Wein, E. Fogel, B. Zukerman, and D. Halperin, Advanced programming techniques applied to Cgal's arrangement package, Computational Geometry, vol.38, issue.1-2, pp.37-63, 2007.
DOI : 10.1016/j.comgeo.2006.11.007

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, pp.997432-7437, 2002.
DOI : 10.1073/pnas.102179699

M. Zacharias, Protein-protein docking with a reduced protein model accounting for side-chain flexibility, Protein Science, vol.238, issue.6, pp.1271-1282, 2003.
DOI : 10.1110/ps.0239303