M. Fromont-racine, J. Rain, and P. Legrain, Toward a functional analysis of the yeast genome through exhaustive two-hybrid screens, Nature Genetics, vol.88, issue.3, pp.277-282, 1997.
DOI : 10.1016/0378-1119(96)00230-2

T. Ito, K. Tashiro, S. Muta, R. Ozawa, T. Chiba et al., Toward a protein-protein interaction map of the budding yeast: A comprehensive system to examine two-hybrid interactions in all possible combinations between the yeast proteins, Proceedings of the National Academy of Sciences, vol.97, issue.3, pp.1143-1150, 2000.
DOI : 10.1073/pnas.97.3.1143

P. Uetz, L. Giot, G. Cagney, T. A. Mansfield, R. S. Judson et al., A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae, Nature, vol.403, pp.623-630, 2000.

H. Yu, P. Braun, M. Yildirim, I. Lemmens, K. Venkatesan et al., High-Quality Binary Protein Interaction Map of the Yeast Interactome Network, Science, vol.322, issue.5898, pp.104-110, 2008.
DOI : 10.1126/science.1158684

Y. Ho, A. Gruhler, A. Heilbut, G. D. Bader, L. Moore et al., Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry, Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry, pp.180-183, 2002.
DOI : 10.1038/415180a

A. C. Gavin, M. Bosche, R. Krause, P. Grandi, M. Marzioch et al., Functional organization of the yeast proteome by systematic analysis of protein complexes, Nature, vol.415, issue.6868, pp.141-148, 2002.
DOI : 10.1038/415141a

P. Aloy and R. Russel, Structural systems biology: modelling protein interactions, Nature Reviews Molecular Cell Biology, vol.3, issue.3, pp.188-197, 2008.
DOI : 10.1038/nrm1859

B. Shoemaker and A. Pachenko, Deciphering Protein???Protein Interactions. Part I. Experimental Techniques and Databases, PLoS Computational Biology, vol.22, issue.3, p.42, 2007.
DOI : 1367-4803(2006)022[0997:TDWRTP]2.0.CO;2

B. Shoemaker and A. Pachenko, Deciphering Protein???Protein Interactions. Part II. Computational Methods to Predict Protein and Domain Interaction Partners, PLoS Computational Biology, vol.21, issue.4, p.43, 2007.
DOI : 1367-4803(2005)021[0993:SAODII]2.0.CO;2

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

P. Chakrabarti and J. Janin, Dissecting protein-protein recognition sites, Proteins: Structure, Function, and Genetics, vol.11, issue.3, pp.334-377, 2002.
DOI : 10.1002/prot.10085

J. Janin and S. J. Wodak, Introduction, Adv Protein Chem, vol.61, pp.1-8, 2002.
DOI : 10.1016/S0065-3233(02)61000-9

URL : https://hal.archives-ouvertes.fr/ird-00653152

J. Janin, Assessing predictions of protein-protein interaction: The CAPRI experiment, Protein Science, vol.14, issue.2, pp.278-83, 2005.
DOI : 10.1110/ps.041081905

J. Bernauer, A. Poupon, J. Aze, and J. And-janin, A docking analysis of the statistical physics of protein???protein recognition, Physical Biology, vol.2, issue.2, pp.17-23, 2005.
DOI : 10.1088/1478-3975/2/2/S02

URL : https://hal.archives-ouvertes.fr/inria-00431699

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.557-62, 2007.
DOI : 10.1093/bioinformatics/btl654

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

J. Boissonnat, O. Devillers, S. Pion, M. Teillaud, Y. et al., Triangulations in CGAL, Computational Geometry, vol.22, issue.1-3
DOI : 10.1016/S0925-7721(01)00054-2

URL : https://hal.archives-ouvertes.fr/hal-01179408

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.121-157, 1996.
DOI : 10.1006/jmbi.1996.0628

H. Hwang, B. Pierce, J. Mintseris, J. Janin, and Z. Weng, Protein-protein docking benchmark version 3.0, Proteins: Structure, Function, and Bioinformatics, vol.69, issue.3, pp.705-709, 2008.
DOI : 10.1002/prot.22106

R. Mendez, R. Leplae, M. F. Lensink, and S. J. Wodak, Assessment of CAPRI predictions in rounds 3-5 shows progress in docking procedures, Proteins: Structure, Function, and Bioinformatics, vol.13, issue.Suppl 6, pp.150-69, 2005.
DOI : 10.1002/prot.20551

J. Bernauer, R. Bahadur, F. Rodier, J. Janin, A. et al., DiMoVo: a Voronoi tessellation-based method for discriminating crystallographic and biological protein-protein interactions, Bioinformatics, vol.24, issue.5, pp.652-658, 2008.
DOI : 10.1093/bioinformatics/btn022

URL : https://hal.archives-ouvertes.fr/inria-00431696