T. Ito, T. Chiba, R. Ozawa, M. Yoshida, M. Hattori et al., A comprehensive two-hybrid analysis to explore the yeast protein interactome, Proceedings of the National Academy of Sciences, vol.98, issue.8, pp.4569-4574, 2001.
DOI : 10.1073/pnas.061034498

Y. Ho, Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry, Nature, vol.415, issue.6868, pp.180-183, 2002.
DOI : 10.1038/415180a

P. Braun, 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

E. Harrington, L. Jensen, and P. Bork, Predicting biological networks from genomic data, FEBS Letters, vol.23, issue.8, pp.1251-1258, 2008.
DOI : 10.1016/j.febslet.2008.02.033

T. Dandekar, B. Snel, M. Huynen, and P. Bork, Conservation of gene order: a fingerprint of proteins that physically interact, Trends in Biochemical Sciences, vol.23, issue.9, pp.324-328, 1998.
DOI : 10.1016/S0968-0004(98)01274-2

M. Galperin and E. Koonin, Who's your neighbor? New computational approaches for functional genomics, Nature Biotechnology, vol.14, issue.6, pp.609-613, 2000.
DOI : 10.1038/76443

C. Marcotte and E. Marcotte, Predicting functional linkages from gene fusions with confidence, Applied bioinformatics, vol.1, issue.2, pp.93-100, 2002.

M. Pellegrini, E. Marcotte, M. Thompson, D. Eisenberg, and T. Yeates, Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles, Proceedings of the National Academy of Sciences, vol.96, issue.8, pp.4285-4288, 1999.
DOI : 10.1073/pnas.96.8.4285

A. Valencia and F. Pazos, Computational methods for the prediction of protein interactions, Current Opinion in Structural Biology, vol.12, issue.3, pp.368-373, 2002.
DOI : 10.1016/S0959-440X(02)00333-0

F. Pazos and A. Valencia, In silico two-hybrid system for the selection of physically interacting protein pairs, Proteins: Structure, Function, and Genetics, vol.20, issue.2, pp.219-227, 2002.
DOI : 10.1002/prot.10074

C. Yeang and D. Haussler, Detecting Coevolution in and among Protein Domains, PLoS Comput Biol, vol.11, issue.311, p.17983264, 2007.

D. Juan, F. Pazos, and A. Valencia, High-confidence prediction of global interactomes based on genome-wide coevolutionary networks, Proceedings of the National Academy of Sciences, vol.105, issue.3, pp.934-939, 2008.
DOI : 10.1073/pnas.0709671105

D. De-juan, F. Pazos, and A. Valencia, Emerging methods in protein co-evolution, Nature Reviews Genetics, vol.485, issue.4, p.23458856, 2013.
DOI : 10.1371/journal.pgen.1000570

M. Weigt, R. White, H. Szurmant, J. Hoch, and T. Hwa, Identification of direct residue contacts in protein-protein interaction by message passing, Proceedings of the National Academy of Sciences, vol.106, issue.1, pp.67-72, 2009.
DOI : 10.1073/pnas.0805923106

F. Morcos, A. Pagnani, B. Lunt, A. Bertolino, D. Marks et al., Direct-coupling analysis of residue coevolution captures native contacts across many protein families, Proceedings of the National Academy of Sciences, vol.108, issue.49, pp.1293-1301, 2011.
DOI : 10.1073/pnas.1111471108

R. Finn, A. Bateman, J. Clements, P. Coggill, R. Eberhardt et al., Pfam: the protein families database, Nucleic Acids Research, vol.42, issue.D1, pp.222-230, 2014.
DOI : 10.1093/nar/gkt1223
URL : https://hal.archives-ouvertes.fr/hal-01294685

M. Ekeberg, C. Lövkvist, Y. Lan, M. Weigt, and E. Aurell, Improved contact prediction in proteins: Using pseudolikelihoods to infer Potts models, Physical Review E, vol.87, issue.1, pp.12707-12717, 2013.
DOI : 10.1103/PhysRevE.87.012707

C. Baldassi, M. Zamparo, C. Feinauer, A. Procaccini, R. Zecchina et al., Fast and Accurate Multivariate Gaussian Modeling of Protein Families: Predicting Residue Contacts and Protein-Interaction Partners, PLoS ONE, vol.36, issue.3, p.24663061
DOI : 10.1371/journal.pone.0092721.s001
URL : https://hal.archives-ouvertes.fr/hal-01344551

S. Balakrishnan, H. Kamisetty, J. Carbonell, S. Lee, and C. Langmead, Learning generative models for protein fold families, Proteins: Structure, Function, and Bioinformatics, vol.34, issue.4, 2011.
DOI : 10.1002/prot.22934

T. Hopf, C. Schärfe, J. Rodrigues, A. Green, O. Kohlbacher et al., Sequence coevolution gives 3D contacts and structures of protein complexes, p.25255213

A. Schug, M. Weigt, J. Onuchic, T. Hwa, and H. Szurmant, High-resolution protein complexes from integrating genomic information with molecular simulation, Proceedings of the National Academy of Sciences, vol.106, issue.52, pp.22124-22129, 2009.
DOI : 10.1073/pnas.0912100106

A. Dago, A. Schug, A. Procaccini, J. Hoch, M. Weigt et al., Structural basis of histidine kinase autophosphorylation deduced by integrating genomics, molecular dynamics, and mutagenesis, Proceedings of the National Academy of Sciences, vol.109, issue.26, pp.1733-1742, 2012.
DOI : 10.1073/pnas.1201301109

L. Burger and E. Van-nimwegen, Accurate prediction of protein???protein interactions from sequence alignments using a Bayesian method, Molecular Systems Biology, vol.8, issue.165, pp.165-175, 2008.
DOI : 10.1038/msb4100203

A. Procaccini, B. Lunt, H. Szurmant, T. Hwa, and M. Weigt, Dissecting the Specificity of Protein-Protein Interaction in Bacterial Two-Component Signaling: Orphans and Crosstalks, PLoS ONE, vol.36, issue.5, p.21573011, 2011.
DOI : 10.1371/journal.pone.0019729.s008

R. Cheng, F. Morcos, H. Levine, and J. Onuchic, Toward rationally redesigning bacterial two-component signaling systems using coevolutionary information, Proceedings of the National Academy of Sciences, vol.111, issue.5, pp.563-571, 2014.
DOI : 10.1073/pnas.1323734111

T. Knöchel, A. Ivens, G. Hester, A. Gonzalez, R. Bauerle et al., The crystal structure of anthranilate synthase from Sulfolobus solfataricus: Functional implications, Proceedings of the National Academy of Sciences, vol.96, issue.17, pp.9479-9484, 1999.
DOI : 10.1073/pnas.96.17.9479

M. Weyand, I. Schlichting, A. Marabotti, and A. Mozzarelli, Crystal Structures of a New Class of Allosteric Effectors Complexed to Tryptophan Synthase, Journal of Biological Chemistry, vol.277, issue.12, pp.10647-10652, 2002.
DOI : 10.1074/jbc.M111285200

T. Consortium, UniProt: a hub for protein information Available from: http://nar.oxfordjournals.org/content, Nucleic Acids Research, vol.4343, issue.D1, pp.204-212, 2015.

C. Feinauer, M. Skwark, A. Pagnani, and E. Aurell, Improving Contact Prediction along Three Dimensions, PLoS Computational Biology, vol.24, issue.10, p.25299132
DOI : 10.1371/journal.pcbi.1003847.s002

K. Katoh, K. Misawa, K. Ki, and T. Miyata, MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic acids research, pp.3059-3066, 2002.

R. Finn, J. Clements, and S. Eddy, HMMER web server: interactive sequence similarity searching. Nucleic acids research, 2011.

N. Nehrt, W. Clark, P. Radivojac, and M. Hahn, Testing the ortholog conjecture with comparative functional genomic data from mammals. PLoS computational biology, ):e1002073. Available from, p.21695233, 2011.

A. Altenhoff, R. Studer, M. Robinson-rechavi, and C. Dessimoz, Resolving the Ortholog Conjecture: Orthologs Tend to Be Weakly, but Significantly, More Similar in Function than Paralogs, PLoS Computational Biology, vol.7, issue.5, p.22615551
DOI : 10.1371/journal.pcbi.1002514.s022

R. Overbeek, M. Fonstein, D. Souza, M. Pusch, G. Maltsev et al., The use of gene clusters to infer functional coupling, Proceedings of the National Academy of Sciences, vol.96, issue.6, pp.2896-2901, 1999.
DOI : 10.1073/pnas.96.6.2896

W. Lathe, B. Snel, and P. Bork, Gene context conservation of a higher order than operons, Trends in Biochemical Sciences, vol.25, issue.10, pp.474-479, 2000.
DOI : 10.1016/S0968-0004(00)01663-7

I. Rogozin, K. Makarova, Y. Wolf, and E. Koonin, Computational approaches for the analysis of gene neighbourhoods in prokaryotic genomes, Briefings in Bioinformatics, vol.5, issue.2, pp.131-149, 2004.
DOI : 10.1093/bib/5.2.131

A. Wlodawer, J. Walter, R. Huber, and L. Sjölin, Structure of bovine pancreatic trypsin inhibitor, Journal of Molecular Biology, vol.180, issue.2, pp.301-329, 1984.
DOI : 10.1016/S0022-2836(84)80006-6

M. Borovinskaya, Structural basis for aminoglycoside inhibition of bacterial ribosome recycling, Nature Structural & Molecular Biology, vol.50, issue.8, pp.727-732, 1271.
DOI : 10.1016/S0076-6879(97)77027-7

M. Wilmanns, J. Priestle, T. Niermann, and J. Jansonius, Three-dimensional structure of the bifunctional enzyme phosphoribosylanthranilate isomerase: Indoleglycerolphosphate synthase from Escherichia coli refined at 2.0 ?? resolution, Journal of Molecular Biology, vol.223, issue.2, pp.477-5070022, 1992.
DOI : 10.1016/0022-2836(92)90665-7