R. Bahadur, P. Chakrabarti, F. Rodier, and J. Janin, A Dissection of Specific and Non-specific Protein???Protein Interfaces, Journal of Molecular Biology, vol.336, issue.4, pp.943-955, 2004.
DOI : 10.1016/j.jmb.2003.12.073

D. Blow, Outline of crystallography for biologists, 2002.

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

L. Bonetta, Protein???protein interactions: Interactome under construction, Nature, vol.464, issue.7325, pp.851-854, 2010.
DOI : 10.1038/468851a

B. Bouvier, R. Grunberg, M. Nilgès, and F. Cazals, Shelling the Voronoi interface of protein-protein complexes reveals patterns of residue conservation, dynamics, and composition, Proteins: Structure, Function, and Bioinformatics, vol.2, issue.3, pp.677-692, 2009.
DOI : 10.1002/prot.22381
URL : https://hal.archives-ouvertes.fr/hal-00796032

B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan et al., CHARMM: A program for macromolecular energy, minimization, and dynamics calculations . journal of computational chemistry, pp.187-217, 1983.

F. Cazals and T. Dreyfus, SBL, the Structural Bioinformatics Library, 2015.

F. Cazals, T. Dreyfus, D. Mazauric, A. Roth, and C. H. Robert, Conformational ensembles and sampled energy landscapes: Analysis and comparison, Journal of Computational Chemistry, vol.32, issue.16, pp.1213-1231, 2015.
DOI : 10.1002/jcc.23913
URL : https://hal.archives-ouvertes.fr/hal-01076317

F. Cazals, H. Kanhere, and S. Loriot, Computing the volume of a union of balls, ACM Transactions on Mathematical Software, vol.38, issue.1, pp.1-20, 2011.
DOI : 10.1145/2049662.2049665
URL : https://hal.archives-ouvertes.fr/hal-00849809

F. Cazals, F. Proust, R. Bahadur, and J. Janin, Revisiting the Voronoi description of protein-protein interfaces, Protein Science, vol.15, issue.9, pp.2082-2092, 2006.
DOI : 10.1110/ps.062245906
URL : https://hal.archives-ouvertes.fr/hal-00796062

T. C. Chalikian, Volumetric properties of proteins. Annual review of biophysics and biomolecular structure, pp.207-235, 2003.

C. A. Chia-en, W. Chen, and M. K. Gilson, Ligand configurational entropy and protein binding, pp.1534-1539, 2007.

C. Chipot, Frontiers in free-energy calculations of biological systems, Wiley Interdisciplinary Reviews: Computational Molecular Science, vol.9, issue.1, pp.71-89, 2014.
DOI : 10.1002/wcms.1157

D. John, . Chodera, L. David, and . Mobley, Entropy-enthalpy compensation: role and ramifications in biomolecular ligand recognition and design, Biophysics, p.42, 2013.

C. Chothia and J. Janin, Principles of protein???protein recognition, Nature, vol.71, issue.5520, pp.705-708, 1975.
DOI : 10.1038/256705a0

W. Cornell, P. Cieplak, C. Bayly, I. Gould, K. Merz et al., A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules, 17] DWJ. Cruickshank. Remarks about protein structure precision, pp.5179-5197, 1995.
DOI : 10.1021/ja00124a002

J. Dunitz, Win some, lose some: enthalpy-entropy compensation in weak intermolecular interactions, Chemistry & Biology, vol.2, issue.11, pp.709-712, 1995.
DOI : 10.1016/1074-5521(95)90097-7

D. Eisenberg and A. D. Mclachlan, Solvation energy in protein folding and binding, Nature, vol.32, issue.6050, pp.199-203, 1986.
DOI : 10.1038/319199a0

D. Eisenberg, M. Wesson, and M. Yamashita, Interpretation of protein folding and binding with atomic solvation parameters, Chem. Scr. A, vol.29, pp.217-221, 1989.

A. Erijman, E. Rosenthal, and J. M. Shifman, How structure defines affinity in proteinprotein interaction, PLOS one, vol.9, issue.10, p.2014

D. Frenkel and B. Smit, Understanding Molecular Simulation, Computers in Physics, vol.11, issue.4, 2002.
DOI : 10.1063/1.4822570

M. Gerstein and F. M. Richards, Protein geometry: volumes, areas and distances, The international tables for crystallography, pp.531-539, 2001.
DOI : 10.1107/97809553602060000885

M. K. Gilson and H. Zhou, Calculation of protein-ligand binding affinities. Annual review of biophysics and biomolecular structure, p.21, 2007.

A. Golbraikh and A. Tropsha, Beware of q2!, Journal of Molecular Graphics and Modelling, vol.20, issue.4, pp.269-276, 2002.
DOI : 10.1016/S1093-3263(01)00123-1

M. Guharoy and P. Chakrabarti, Conservation and relative importance of residues across protein-protein interfaces, Proceedings of the National Academy of Sciences, vol.102, issue.43, pp.15447-15452, 2005.
DOI : 10.1073/pnas.0505425102

W. F. Van-gunsteren and H. J. Berendsen, Groningen molecular simulation (GROMOS) Library manual, pp.1-221, 1987.

L. Györfi and A. Krzyzak, A distribution-free theory of nonparametric regression, 2002.
DOI : 10.1007/b97848

N. Horton and M. Lewis, Calculation of the free energy of association for protein complexes, Protein Science, vol.21, issue.1, pp.169-181, 1992.
DOI : 10.1002/pro.5560010117

J. Janin, A minimal model of protein-protein binding affinities, Protein Science, vol.2, issue.12, pp.1813-1817, 2014.
DOI : 10.1002/pro.2560

J. Janin, R. P. Bahadur, and P. Chakrabarti, Protein???protein interaction and quaternary structure, Quarterly Reviews of Biophysics, vol.31, issue.02, pp.133-180, 2008.
DOI : 10.1073/pnas.93.19.10167

P. L. Kastritis, I. H. Moal, H. Hwang, Z. Weng, P. A. Bates et al., A structure-based benchmark for protein-protein binding affinity, Protein Science, vol.3, issue.3, pp.482-491, 2011.
DOI : 10.1002/pro.580

P. L. Kastritis, J. P. Rodrigues, G. E. Folkers, R. Boelens, and A. M. Bonvin, Proteins Feel More Than They See: Fine-Tuning of Binding Affinity by Properties of the Non-Interacting Surface, Journal of Molecular Biology, vol.426, issue.14, pp.2632-2652, 2014.
DOI : 10.1016/j.jmb.2014.04.017

S. M. Lippow, K. D. Wittrup, and B. Tidor, Computational design of antibody-affinity improvement beyond in vivo maturation, Nature Biotechnology, vol.103, issue.10, pp.1171-1176, 2007.
DOI : 10.1038/nbt1336

S. Loriot and F. Cazals, Modeling macro-molecular interfaces with Intervor, Bioinformatics, vol.26, issue.7, pp.964-965, 2010.
DOI : 10.1093/bioinformatics/btq052
URL : https://hal.archives-ouvertes.fr/hal-00849822

M. Lu and J. Ma, The Role of Shape in Determining Molecular Motions, Biophysical Journal, vol.89, issue.4, pp.2395-2401, 2005.
DOI : 10.1529/biophysj.105.065904

G. Meng, N. Arkus, M. P. Brenner, and V. N. Manoharan, The Free-Energy Landscape of Clusters of Attractive Hard Spheres, Science, vol.327, issue.5965, pp.327560-563, 2010.
DOI : 10.1126/science.1181263

I. Moal and J. Fernández-recio, Comment on 'protein-protein binding affinity prediction from amino acid sequence', Bioinformatics, vol.31, issue.4, p.2014
DOI : 10.1093/bioinformatics/btu682

I. H. Moal, R. Agius, and P. A. Bates, Protein-protein binding affinity prediction on a diverse set of structures, Bioinformatics, vol.27, issue.21, pp.3002-3009, 2011.
DOI : 10.1093/bioinformatics/btr513

I. Moreira, P. Fernandes, and M. J. Ramos, Hot spots-A review of the protein-protein interface determinant amino-acid residues, Proteins: Structure, Function, and Bioinformatics, vol.117, issue.4, pp.803-812, 2007.
DOI : 10.1002/prot.21396

B. Phipson and G. K. Smyth, Permutation P-values Should Never Be Zero: Calculating Exact P-values When Permutations Are Randomly Drawn, Statistical Applications in Genetics and Molecular Biology, vol.9, issue.1, 2010.
DOI : 10.2202/1544-6115.1585

P. Privalov, A. Dragan, and C. Crane-robinson, Interpreting protein/dna interactions: distinguishing specific from non-specific and electrostatic from non-electrostatic components. Nucleic acids research, p.984, 2010.

D. Rajamani, S. Thiel, S. Vajda, and C. J. Camacho, Anchor residues in protein-protein interactions, Proceedings of the National Academy of Sciences, vol.101, issue.31, pp.11287-11292, 2004.
DOI : 10.1073/pnas.0401942101

G. Subba-rao, R. Vijayakrishnan, and M. Kumar, Structure-based design of a novel class of potent inhibitors of inha, the enoyl acyl carrier protein reductase from mycobacterium tuberculosis: A computer modelling approach, Chemical biology & drug design, issue.5, pp.72444-449, 2008.

F. Rodier, R. P. Bahadur, P. Chakrabarti, and J. Janin, Hydration of protein-protein interfaces, Proteins: Structure, Function, and Bioinformatics, vol.280, issue.1, pp.36-45, 2005.
DOI : 10.1002/prot.20478

H. Schiessel, Counterion Condensation on Flexible Polyelectrolytes:?? Dependence on Ionic Strength and Chain Concentration, Macromolecules, vol.32, issue.17, pp.5673-5680, 1999.
DOI : 10.1021/ma990051k

A. Schmidt, H. Xu, A. Khan, T. O. Donnell, S. Khurana et al., Preconfiguration of the antigen-binding site during affinity maturation of a broadly neutralizing influenza virus antibody, Proceedings of the National Academy of Sciences, vol.110, issue.1, pp.264-269, 2013.
DOI : 10.1073/pnas.1218256109

R. Tibshirani, Regression shrinkage and selection via the lasso, Journal of the Royal Statistical Society. Series B (Methodological), pp.267-288, 1996.

K. M. Visscher, P. L. Kastritis, and A. Bonvin, Non-interacting surface solvation and dynamics in protein-protein interactions, Proteins: Structure, Function, and Bioinformatics, vol.101, issue.3, pp.445-458, 2015.
DOI : 10.1002/prot.24741

D. J. Wales51-]-z, L. Yand, L. Guo, J. Hu, and . Wang, Energy Landscapes Specificity and affinity quantification of protein protein interactions, Bioinformatics, vol.29, issue.9, pp.1127-1133, 2003.