W. R. Taylor, The classification of amino acid conservation, Journal of Theoretical Biology, vol.119, issue.2, pp.205-218, 1986.
DOI : 10.1016/S0022-5193(86)80075-3

B. J. Gellatly and J. L. Finney, Calculation of protein volumes: An alternative to the Voronoi procedure, Journal of Molecular Biology, vol.161, issue.2, pp.305-322, 1982.
DOI : 10.1016/0022-2836(82)90155-3

Y. Harpaz, M. Gerstein, and C. Chothia, Volume changes on protein folding, Structure, vol.2, issue.7, pp.641-649, 1994.
DOI : 10.1016/S0969-2126(00)00065-4

J. Pontius, J. Richelle, and S. J. Wodak, Deviations from Standard Atomic Volumes as a Quality Measure for Protein Crystal Structures, Journal of Molecular Biology, vol.264, issue.1, pp.121-136, 1996.
DOI : 10.1006/jmbi.1996.0628

F. M. Richards, The interpretation of protein structures: Total volume, group volume distributions and packing density, Journal of Molecular Biology, vol.82, issue.1, pp.1-14, 1974.
DOI : 10.1016/0022-2836(74)90570-1

J. Tsai, R. Taylor, C. Chothia, and M. Gerstein, The packing density in proteins: standard radii and volumes, Journal of Molecular Biology, vol.290, issue.1, pp.253-266, 1999.
DOI : 10.1006/jmbi.1999.2829

A. A. Zamyatnin, Amino Acid, Peptide, and Protein Volume in Solution, Annual Review of Biophysics and Bioengineering, vol.13, issue.1, pp.145-165, 1984.
DOI : 10.1146/annurev.bb.13.060184.001045

A. Soyer, J. Chomilier, J. P. Mornon, R. Jullien, and J. F. Sadoc, Vorono?? Tessellation Reveals the Condensed Matter Character of Folded Proteins, Physical Review Letters, vol.85, issue.16, pp.3532-3535, 2000.
DOI : 10.1103/PhysRevLett.85.3532

A. Goede, R. Preissner, and C. Frommel, Voronoi cell: New method for allocation of space among atoms: Elimination of avoidable errors in calculation of atomic volume and density, Journal of Computational Chemistry, vol.247, issue.9, pp.1113-1123, 1997.
DOI : 10.1002/(SICI)1096-987X(19970715)18:9<1113::AID-JCC1>3.0.CO;2-U

B. Angelov, J. F. Sadoc, R. Jullien, A. Soyer, J. P. Mornon et al., Nonatomic solvent-driven voronoi tessellation of proteins: An open tool to analyze protein folds, Proteins: Structure, Function, and Genetics, vol.307, issue.4, pp.446-456, 2002.
DOI : 10.1002/prot.10220

URL : https://hal.archives-ouvertes.fr/hal-01215355

B. J. Mcconkey, V. Sobolev, and M. Edelman, Quantification of protein surfaces, volumes and atom-atom contacts using a constrained Voronoi procedure, Bioinformatics, vol.18, issue.10, pp.1365-1373, 2002.
DOI : 10.1093/bioinformatics/18.10.1365

J. F. Sadoc, R. Jullien, and N. Rivier, The Laguerre polyhedral decomposition: application to protein folds, The European Physical Journal B - Condensed Matter, vol.33, issue.3, pp.355-363, 2003.
DOI : 10.1140/epjb/e2003-00176-5

M. Gerstein, J. Tsai, and M. Levitt, The Volume of Atoms on the Protein Surface: Calculated from Simulation, using Voronoi Polyhedra, Journal of Molecular Biology, vol.249, issue.5, pp.955-966, 1995.
DOI : 10.1006/jmbi.1995.0351

A. Poupon, Voronoi and Voronoi-related tessellations in studies of protein structure and interaction, Current Opinion in Structural Biology, vol.14, issue.2, pp.233-241, 2004.
DOI : 10.1016/j.sbi.2004.03.010

C. Chothia, Structural invariants in protein folding, Nature, vol.29, issue.5498, pp.304-308, 1975.
DOI : 10.1038/254304a0

J. Janin and C. Chothia, The structure of protein-protein recognition sites, J. Biol. Chem, vol.265, pp.16027-16030, 1990.

M. Gerstein and C. Chothia, Packing at the protein-water interface., Proc. Natl. Acad
DOI : 10.1073/pnas.93.19.10167

J. Liang, H. Edelsbrunner, P. Fu, P. V. Sudhakar, and S. Subramaniam, Analytical shape computation of macromolecules: I. molecular area and volume through alpha shape, Proteins: Structure, Function, and Genetics, vol.9, issue.1, pp.1-17, 1998.
DOI : 10.1002/(SICI)1097-0134(19981001)33:1<1::AID-PROT1>3.0.CO;2-O

J. Liang, H. Edelsbrunner, P. Fu, P. V. Sudhakar, and S. Subramaniam, Analytical shape computation of macromolecules: II. Inaccessible cavities in proteins, Proteins: Structure, Function, and Genetics, vol.70, issue.1, pp.18-29, 1998.
DOI : 10.1002/(SICI)1097-0134(19981001)33:1<18::AID-PROT2>3.0.CO;2-H

K. Rother, P. W. Hildebrand, A. Goede, B. Gruening, and R. Preissner, Voronoia: analyzing packing in protein structures, Nucleic Acids Research, vol.37, issue.Database, pp.393-395, 2009.
DOI : 10.1093/nar/gkn769

URL : http://doi.org/10.1093/nar/gkn769

F. Dupuis, J. F. Sadoc, and J. P. Mornon, Protein secondary structure assignment through Vorono?? tessellation, Proteins: Structure, Function, and Bioinformatics, vol.13, issue.3, pp.519-528, 2004.
DOI : 10.1002/prot.10566

URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=

F. Birzele, J. E. Gewehr, G. Csaba, and R. Zimmer, Vorolign--fast structural alignment using Voronoi contacts, Bioinformatics, vol.23, issue.2, pp.205-211, 2007.
DOI : 10.1093/bioinformatics/btl294

J. Bernauer, J. Azé, J. Janin, and A. Poupon, A new protein protein docking scoring function based on interface residue properties, Bioinformatics, vol.23, issue.5, pp.555-562, 2007.
DOI : 10.1093/bioinformatics/btl654

URL : https://hal.archives-ouvertes.fr/inria-00431697

N. Kobayashi and N. Go, A method to search for similar protein local structures at ligand-binding sites and its application to adenine recognition, European Biophysics Journal, vol.26, issue.2, pp.135-144, 1997.
DOI : 10.1007/s002490050065

W. R. Taylor, Protein structural domain identification, Protein Engineering Design and Selection, vol.12, issue.3, pp.203-216, 1999.
DOI : 10.1093/protein/12.3.203

H. Wako and T. Yamato, Novel method to detect a motif of local structures in different protein conformations, Protein Engineering Design and Selection, vol.11, issue.11, pp.981-990, 1998.
DOI : 10.1093/protein/11.11.981

J. Huan, D. Bandyopadhyay, W. Wang, J. Snoeyink, J. Prins et al., Comparing Graph Representations of Protein Structure for Mining Family-Specific Residue-Based Packing Motifs, Journal of Computational Biology, vol.12, issue.6, pp.657-671, 2005.
DOI : 10.1089/cmb.2005.12.657

DOI : 10.1142/9789812704856_0039

T. Taylor, M. Rivera, and G. Wilson, Vaisman, II, New method for protein secondary structure assignment based on a simple topological descriptor Bioinformatics;Four-body scoring function for mutagenesis, Proteins Deutsch, C.; Krishnamoorthy, B., Bioinformatics, vol.60, issue.23, pp.513-524, 2005.

V. A. Ilyin, A. Abyzov, and C. M. Leslin, Structural alignment of proteins by a novel TOPOFIT method, as a superimposition of common volumes at a topomax point, Protein Science, vol.134, issue.7, pp.1865-1874, 2004.
DOI : 10.1110/ps.04672604

J. Roach, S. Sharma, M. Kapustina, C. W. Carter, and . Jr, Structure alignment via Delaunay tetrahedralization, Proteins: Structure, Function, and Bioinformatics, vol.277, issue.1, pp.66-81, 2005.
DOI : 10.1002/prot.20479

C. W. Carter, . Jr, B. C. Lefebvre, S. A. Cammer, A. Tropsha et al., Four-body potentials reveal protein-specific correlations to stability changes caused by hydrophobic core mutations, Journal of Molecular Biology, vol.311, issue.4, pp.625-638, 2001.
DOI : 10.1006/jmbi.2001.4906

H. H. Gan, A. Tropsha, T. Schlick, and A. Tropsha, Lattice protein folding with two and four-body statistical potentials, Proteins: Structure, Function, and Genetics, vol.23, issue.2, pp.161-174, 2001.
DOI : 10.1002/1097-0134(20010501)43:2<161::AID-PROT1028>3.0.CO;2-F

M. Masso, . Vaisman, . Ii, J. Bacardit, J. D. Hirst et al., Accurate prediction of enzyme mutant activity based on a multibody statistical potential Prediction of topological contacts in proteins using learning classifier systems, Bioinformatics Soft. Comput, vol.23, issue.13, pp.3155-3161, 2007.

R. Zimmer, M. Wohler, and R. Thiele, New scoring schemes for protein fold recognition based on Voronoi contacts, Bioinformatics, vol.14, issue.3, pp.295-308, 1998.
DOI : 10.1093/bioinformatics/14.3.295

S. J. Hubbard, J. M. Thornton, H. M. Berman, J. Westbrook, and H. Weissig, 1.1; Dept of Biochemistry and Molecular Biology: University College London, 1993. 41

I. N. Shindyalov and P. E. Bourne, The Protein Data Bank, Nucleic Acids Res, vol.28, pp.235-242, 2000.

G. Wang, R. L. Dunbrack, and . Jr, PISCES: a protein sequence culling server, Bioinformatics, vol.19, issue.12
DOI : 10.1093/bioinformatics/btg224

G. Wang, R. L. Dunbrack, and . Jr, PISCES: recent improvements to a PDB sequence culling server, Nucleic Acids Research, vol.33, issue.Web Server, pp.94-98, 2005.
DOI : 10.1093/nar/gki402

P. B. Finer-moore, J. S. Kossiakoff, A. A. Hurley, J. H. Earnest, T. Stroud et al., Flexibility of the DNA-binding domains of trp repressor Solvent structure in crystals of trypsin determined by X-ray and neutron diffraction, Proteins Proteins, vol.3, issue.12, pp.18-31, 1988.

H. J. Berendsen, D. Van-der-spoel, and R. Van-drunen, GROMACS: A message-passing parallel molecular dynamics implementation, Computer Physics Communications, vol.91, issue.1-3, pp.43-56, 1995.
DOI : 10.1016/0010-4655(95)00042-E

B. Hess, C. Kutzner, D. Van-der-spoel, and E. Lindahl, GROMACS 4:?? Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation, Journal of Chemical Theory and Computation, vol.4, issue.3, pp.435-447, 2008.
DOI : 10.1021/ct700301q

E. Lindahl, B. Hess, and D. Van-der-spoel, GROMACS 3.0: a package for molecular simulation and trajectory analysis, Journal of Molecular Modeling, vol.7, issue.8, pp.306-317, 2001.
DOI : 10.1007/s008940100045

A. E. Mark, W. R. Scott, and I. G. Tironi, Biomolecular Simulation: The GROMOS96 51, Berendsen, H. J. C.; Postma, P. M.; van Gunsteren, W. F, 1981.

H. J. Berendsen, J. P. Postma, W. F. Van-gunsteren, A. Dinola, J. R. Haak et al., Molecular dynamics with coupling to an external bath LINCS: A linear constraint solver for molecular simulations, J. Chem. Phys. J. Comput. Chem, vol.81, issue.18, pp.3684-3690, 1984.

I. G. Tironi, R. Sperb, P. E. Smith, and W. F. Van-gunsteren, A generalized reaction field method for molecular dynamics simulations, The Journal of Chemical Physics, vol.102, issue.13, pp.5451-5459, 1995.
DOI : 10.1063/1.469273

W. Kabsch and C. Sander, Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features, Biopolymers, vol.33, issue.12, pp.2577-2637, 1983.
DOI : 10.1002/bip.360221211

W. L. Delano, The PyMOL Molecular Graphics System on World Wide Web http://www.pymol.org, 2002.

R. K. Singh, A. Tropsha, and K. Sugihara, Delaunay Tessellation of Proteins: Four Body Nearest-Neighbor Propensities of Amino Acid Residues, Journal of Computational Biology, vol.3, issue.2, pp.213-221, 1996.
DOI : 10.1089/cmb.1996.3.213

C. H. Kim, C. I. Won, Y. Cho, D. Kim, S. Lee et al., Interaction interfaces in proteins via the Voronoi diagram of atoms, Computer-Aided Design, vol.38, issue.11, pp.1192-1204, 2006.
DOI : 10.1016/j.cad.2006.07.007

M. Allaire, Y. Li, R. E. Mackenzie, and M. Cygler, The 3-D structure of a folate-dependent dehydrogenase/cyclohydrolase bifunctional enzyme at 1.5 ?? resolution, Structure, vol.6, issue.2, pp.173-182, 1998.
DOI : 10.1016/S0969-2126(98)00019-7

J. Fauchere and V. Pliska, Hydrophobic parameters pi of amino-acid side chains from the partitioning of N-acetyl-amino-acid amides, Eur.J.Med.Chem. -Chim. Ther, vol.18, pp.369-375, 1983.

M. Lobanov, N. S. Bogatyreva, and O. V. Galzitskaia, Radius of gyration as an indicator of protein structure compactness, Molecular Biology, vol.42, issue.4, pp.701-706, 2008.
DOI : 10.1134/S0026893308040195

S. O. Garbuzynskiy, More compact protein globules exhibit slower folding rates, Proteins, vol.70, pp.329-332, 2008.

D. N. Ivankov, S. O. Garbuzynskiy, E. Alm, K. W. Plaxco, D. Baker et al., Contact order revisited: Influence of protein size on the folding rate, Protein Science, vol.96, issue.9, pp.2057-2062, 2003.
DOI : 10.1110/ps.0302503

P. J. Fleming and F. M. Richards, Protein packing: dependence on protein size, secondary structure and amino acid composition, Journal of Molecular Biology, vol.299, issue.2, pp.487-498, 2000.
DOI : 10.1006/jmbi.2000.3750

T. E. Creighton, The polymeric nature of proteins, PROTEINS: Structures and Molecular Properties, 1992.

K. Gekko and H. Noguchi, Compressibility of globular proteins in water at 25.degree.C, The Journal of Physical Chemistry, vol.83, issue.21
DOI : 10.1021/j100484a006

P. G. Squire and M. E. Himmel, Hydrodynamics and protein hydration, Archives of Biochemistry and Biophysics, vol.196, issue.1
DOI : 10.1016/0003-9861(79)90563-0

J. C. Gelly, C. Etchebest, S. Hazout, and A. G. De-brevern, Protein Peeling 2: a web server to convert protein structures into series of protein units, Nucleic Acids Research, vol.34, issue.Web Server, pp.75-78, 2006.
DOI : 10.1093/nar/gkl292

URL : https://hal.archives-ouvertes.fr/inserm-00133731

U. Samanta, R. P. Bahadur, and P. Chakrabarti, Quantifying the accessible surface area of protein residues in their local environment, Protein Engineering Design and Selection, vol.15, issue.8, pp.659-667, 2002.
DOI : 10.1093/protein/15.8.659

G. Faure, A. Bornot, and A. G. De-brevern, Protein contacts, inter-residue interactions and side-chain modelling, Biochimie, vol.90, issue.4, pp.626-639, 2008.
DOI : 10.1016/j.biochi.2007.11.007

URL : https://hal.archives-ouvertes.fr/inserm-00189828

A. A. Canutescu, A. A. Shelenkov, R. L. Dunbrack, and . Jr, A graph-theory algorithm for rapid protein side-chain prediction, Protein Science, vol.311, issue.9, 2001.
DOI : 10.1110/ps.03154503

G. G. Krivov, M. V. Shapovalov, R. L. Dunbrack, and . Jr, Improved prediction of protein side-chain conformations with SCWRL4, Proteins: Structure, Function, and Bioinformatics, vol.3, issue.Pt 1, pp.778-795, 2009.
DOI : 10.1002/prot.22488

E. Eyal, R. Najmanovich, B. J. Mcconkey, M. Edelman, and V. Sobolev, Importance of solvent accessibility and contact surfaces in modeling side-chain conformations in proteins, Journal of Computational Chemistry, vol.50, issue.5
DOI : 10.1002/jcc.10420

J. Xu, F. Jiao, and B. Berger, A tree-decomposition approach to protein structure prediction, 2005 IEEE Computational Systems Bioinformatics Conference (CSB'05), pp.247-256, 2005.
DOI : 10.1109/CSB.2005.9

G. Faure, A. Bornot, and A. G. De-brevern, Analysis of protein contacts into Protein Units, Biochimie, vol.91, issue.7, pp.876-887, 2009.
DOI : 10.1016/j.biochi.2009.04.008

URL : https://hal.archives-ouvertes.fr/inserm-00375095