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, pp.264-269, 2013.
DOI : 10.1073/pnas.1218256109

F. Alber, F. Förster, D. Korkin, M. Topf, and A. Sali, Integrating Diverse Data for Structure Determination of Macromolecular Assemblies, Annual Review of Biochemistry, vol.77, issue.1, pp.11-12, 2008.
DOI : 10.1146/annurev.biochem.77.060407.135530

O. Puig, The Tandem Affinity Purification (TAP) Method: A General Procedure of Protein Complex Purification, Methods, vol.24, issue.3, pp.218-229, 2001.
DOI : 10.1006/meth.2001.1183

M. Sharon and C. V. Robinson, The Role of Mass Spectrometry in Structure Elucidation of Dynamic Protein Complexes, Annual Review of Biochemistry, vol.76, issue.1, pp.167-193, 2007.
DOI : 10.1146/annurev.biochem.76.061005.090816

R. J. Rose, E. Damoc, E. Denisov, A. Makarov, and A. J. Heck, High-sensitivity Orbitrap mass analysis of intact macromolecular assemblies, Nature Methods, vol.10, issue.11, pp.1084-1086, 2012.
DOI : 10.1021/ac991131p

T. Berggård, S. Linse, and P. James, Methods for the detection and analysis of protein???protein interactions, PROTEOMICS, vol.21, issue.16, pp.2833-2842, 2007.
DOI : 10.1002/pmic.200700131

P. Braun, M. Tasan, M. Dreze, M. Barrios-rodiles, I. Lemmens et al., An experimentally derived confidence score for binary protein-protein interactions, Nature Methods, vol.6, issue.1, pp.91-97, 2008.
DOI : 10.1038/nprot.2006.14

T. Dreyfus, V. Doye, and F. Cazals, Assessing the reconstruction of macromolecular assemblies with toleranced models, Proteins: Structure, Function, and Bioinformatics, vol.109, issue.9, pp.2125-2136, 2012.
DOI : 10.1002/prot.24092

URL : https://hal.archives-ouvertes.fr/hal-00764009

T. Dreyfus, V. Doye, and F. Cazals, Probing a continuum of macro-molecular assembly models with graph templates of sub-complexes, Proteins: structure, function, and bioinformatics, issue.11, pp.812034-2044, 2013.
URL : https://hal.archives-ouvertes.fr/hal-00849795

J. Yu, T. Murali, and R. L. Finley-jr, Assigning Confidence Scores to Protein???Protein Interactions, Two Hybrid Technologies, pp.161-174, 2012.
DOI : 10.1007/978-1-61779-455-1_9

B. Turner, S. Razick, A. L. Turinsky, J. Vlasblom, E. K. Crowdy et al., iRefWeb: interactive analysis of consolidated protein interaction data and their supporting evidence, Database, vol.2010, issue.0, p.23, 2010.
DOI : 10.1093/database/baq023

D. Agarwal, J. Araujo, C. Caillouet, F. Cazals, D. Coudert et al., Connectivity Inference in Mass Spectrometry Based Structure Determination, European Symposium on Algorithms, pp.289-300, 2013.
DOI : 10.1007/978-3-642-40450-4_25

URL : https://hal.archives-ouvertes.fr/hal-00837496

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. Sharon, T. Taverner, X. I. Ambroggio, R. J. Deshaies, and C. V. Robinson, Structural Organization of the 19S Proteasome Lid: Insights from MS of Intact Complexes, PLoS Biology, vol.279, issue.8, p.267, 2006.
DOI : 10.1371/journal.pbio.0040267.t004

M. Zhou, A. M. Sandercock, C. S. Fraser, G. Ridlova, E. Stephens et al., Mass spectrometry reveals modularity and a complete subunit interaction map of the eukaryotic translation factor eIF3, Proc. of the National Academy of Sciences, pp.10518139-18144, 2008.
DOI : 10.1073/pnas.0801313105

H. Hernández, A. Dziembowski, T. Taverner, B. Séraphin, and C. V. Robinson, Subunit architecture of multimeric complexes isolated directly from cells, EMBO reports, vol.7, issue.6, pp.605-610, 2006.
DOI : 10.1016/S0092-8674(01)00592-X

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

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

E. Levy, E. Erba, C. Robinson, and S. Teichmann, Assembly reflects evolution of protein complexes, Nature, vol.2, issue.7199, pp.1262-1265, 2008.
DOI : 10.1038/nature06942

A. Kao, A. Randall, Y. Yang, V. R. Patel, W. Kandur et al., Mapping the Structural Topology of the Yeast 19S Proteasomal Regulatory Particle Using Chemical Cross-linking and Probabilistic Modeling, Molecular & Cellular Proteomics, vol.11, issue.12, 2012.
DOI : 10.1074/mcp.M112.018374

D. L. Makino, M. Baumgärtner, and E. Conti, Crystal structure of an RNA-bound 11-subunit eukaryotic exosome complex, Nature, vol.448, issue.7439, pp.49570-75, 2013.
DOI : 10.1016/j.jmb.2006.09.076

G. C. Lander, E. Estrin, M. E. Matyskiela, C. Bashore, E. Nogales et al., Complete subunit architecture of the proteasome regulatory particle, Nature, vol.157, issue.7384, pp.482186-191, 2012.
DOI : 10.1038/nature10774

K. Lasker, F. Förster, S. Bohn, T. Walzthoeni, E. Villa et al., Molecular architecture of the 26S proteasome holocomplex determined by an integrative approach, Proceedings of the National Academy of Sciences, vol.109, issue.5, pp.1380-1387, 2012.
DOI : 10.1073/pnas.1120559109

J. Querol-audi, C. Sun, J. M. Vogan, M. D. Smith, J. Gu et al., Architecture of Human Translation Initiation Factor 3, Structure, vol.21, issue.6, pp.920-928, 2013.
DOI : 10.1016/j.str.2013.04.002

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