S. R. Kondrashov and . Sunyaev, A method and server for predicting damaging missense mutations, Nat. Methods, vol.7, issue.4, pp.248-249, 2010.

H. Akashi, Within- and between-species DNA sequence variation and the ???footprint??? of natural selection, Gene, vol.238, issue.1, pp.39-51, 1999.
DOI : 10.1016/S0378-1119(99)00294-2

J. Berni, T. Alder, and . Wainwright, Studies in molecular dynamics. i. general method, The Journal of Chemical Physics, vol.31, issue.2, pp.459-466, 1959.

B. Alder and T. Wainwright, Phase Transition for a Hard Sphere System, The Journal of Chemical Physics, vol.27, issue.5, p.1208, 1957.
DOI : 10.1063/1.1743956

A. Allain, I. Chauvot-de-beauchêne, F. Langenfeld, Y. Guarracino, E. Laine et al., Allosteric pathway identification through network analysis: from molecular dynamics simulations to interactive 2D and 3D graphs, Faraday Discuss., vol.15, issue.5, 2014.
DOI : 10.1016/j.cytogfr.2004.09.001

URL : https://hal.archives-ouvertes.fr/hal-01505837

S. F. Altschul, T. L. Madden, A. A. Schaffer, J. Zhang, Z. Zhang et al., Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Research, vol.25, issue.17, pp.253389-3402, 1997.
DOI : 10.1093/nar/25.17.3389

R. William, . Atchley, R. Kurt, . Wollenberg, M. Walter et al., Correlations among amino acid sites in bhlh protein domains: an information theoretic analysis, Molecular biology and evolution, vol.17, issue.1, pp.164-178, 2000.

R. Bahadur and M. Zacharias, The interface of protein-protein complexes: Analysis of contacts and prediction of interactions, Cellular and Molecular Life Sciences, vol.65, issue.7-8, pp.1059-1072, 2008.
DOI : 10.1007/s00018-007-7451-x

Y. Bai, A. Karimi, H. J. Dyson, and P. E. Wright, Absence of a stable intermediate on the folding pathway of protein A, Protein Science, vol.27, issue.7, pp.1449-1457, 1997.
DOI : 10.1111/j.1399-3011.1992.tb00291.x

J. Baussand and A. Carbone, A Combinatorial Approach to Detect Coevolved Amino Acid Networks in Protein Families of Variable Divergence, PLoS Computational Biology, vol.15, issue.1, p.1000488, 2009.
DOI : 10.1371/journal.pcbi.1000488.s002

J. Herman, J. Berendsen, M. Pl, W. F. Postma, . Van-gunsteren et al., Molecular dynamics with coupling to an external bath, The Journal of chemical physics, issue.8, pp.813684-3690, 1984.

H. M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T. N. Bhat et al., The Protein Data Bank, Nucleic Acids Research, vol.28, issue.1, pp.235-242, 2000.
DOI : 10.1093/nar/28.1.235

URL : http://journals.iucr.org/d/issues/2002/06/01/an0594/an0594.pdf

M. Bhattacharyya, C. R. Bhat, and S. Vishveshwara, An automated approach to network features of protein structure ensembles, Protein Science, vol.22, issue.10, pp.1399-1416
DOI : 10.1002/pro.2333

K. Blacklock, M. Gennady, and . Verkhivker, Differential Modulation of Functional Dynamics and Allosteric Interactions in the Hsp90-Cochaperone Complexes with p23 and Aha1: A Computational Study, PLoS ONE, vol.22, issue.3, p.71936, 2013.
DOI : 10.1371/journal.pone.0071936.s004

D. Blocquel, M. Beltrandi, J. Erales, P. Barbier, and S. Longhi, Biochemical and structural studies of the oligomerization domain of the Nipah virus phosphoprotein: Evidence for an elongated coiled-coil homotrimer, Virology, vol.446, issue.1-2, pp.162-172, 2013.
DOI : 10.1016/j.virol.2013.07.031

D. Blocquel, J. Habchi, E. Durand, M. Sevajol, F. Ferron et al., phosphoprotein multimerization domain as an illustrative example, Acta Crystallographica Section D Biological Crystallography, vol.38, issue.6, pp.1589-1603, 2014.
DOI : 10.1107/S139900471400234X/dz5322sup4.avi

A. Bloomer, . Jn-champness, . Bricogne, A. Staden, and . Klug, Protein disk of tobacco mosaic virus at 2.8 ?? resolution showing the interactions within and between subunits, Nature, vol.74, issue.5686, pp.276362-368, 1978.
DOI : 10.1038/265217a0

W. Bode, P. Schwager, and R. Huber, The transition of bovine trypsinogen to a trypsin-like state upon strong ligand binding, Journal of Molecular Biology, vol.118, issue.1, pp.99-112, 1978.
DOI : 10.1016/0022-2836(78)90246-2

C. Boede, . Kovacs, . Szalay, . Palotai, P. Korcsmaros et al., Network analysis of protein dynamics, FEBS Letters, vol.104, issue.15, pp.2776-2782, 2007.
DOI : 10.1073/pnas.0607132104

K. V. Brinda and S. Vishveshwara, A Network Representation of Protein Structures: Implications for Protein Stability, Biophysical Journal, vol.89, issue.6, pp.4159-4170, 2005.
DOI : 10.1529/biophysj.105.064485

C. C. Broder, Henipavirus outbreaks to antivirals: the current status of potential therapeutics, Current Opinion in Virology, vol.2, issue.2, pp.176-187, 2012.
DOI : 10.1016/j.coviro.2012.02.016

J. Celeste, . Brown, K. Audra, K. Johnson, . Dunker et al., Evolution and disorder, Current opinion in structural biology, vol.21, issue.3, pp.441-446, 2011.

F. Jessica, . Bruhn, C. Katherine, J. Barnett, . Bibby et al., Crystal structure of the nipah virus phosphoprotein tetramerization domain, Journal of virology, vol.88, issue.1, pp.758-762, 2014.

A. N. Bullock, J. Henckel, B. S. Dedecker, C. M. Johnson, P. V. Nikolova et al., Thermodynamic stability of wild-type and mutant p53 core domain, Proceedings of the National Academy of Sciences, vol.24, issue.1, pp.9414338-14342, 1997.
DOI : 10.1107/S0021889891004399

URL : http://www.pnas.org/content/94/26/14338.full.pdf

C. D. Bustamante, J. P. Townsend, and D. L. Hartl, Solvent Accessibility and Purifying Selection Within Proteins of Escherichia coli and Salmonella enterica, Molecular Biology and Evolution, vol.17, issue.2, pp.301-308, 2000.
DOI : 10.1093/oxfordjournals.molbev.a026310

URL : https://academic.oup.com/mbe/article-pdf/17/2/301/6395751/mbev_17_02_0301.pdf

J. S. Butler and S. N. Loh, -Dependent Misfolding of the p53 DNA Binding Domain, Biochemistry, vol.46, issue.10, pp.2630-2639, 2007.
DOI : 10.1021/bi062106y

S. Calhoun and V. Daggett, Structural Effects of the L145Q, V157F, and R282W Cancer-Associated Mutations in the p53 DNA-Binding Core Domain, Biochemistry, vol.50, issue.23, pp.5345-5353, 2011.
DOI : 10.1021/bi200192j

J. M. Canadillas, H. Tidow, S. M. Freund, T. J. Rutherford, H. C. Ang et al., Solution structure of p53 core domain: Structural basis for its instability, Proceedings of the National Academy of Sciences, vol.54, issue.Pt 5, pp.2109-2114, 2006.
DOI : 10.1107/S0907444998003254

E. Capriotti, P. Fariselli, and R. Casadio, I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure, Nucleic Acids Research, vol.33, issue.Web Server, pp.306-310, 2005.
DOI : 10.1093/nar/gki375

A. Carbone, Extracting Coevolving Characters from a Tree of Species, Discrete and Topological Models in Molecular Biology, pp.45-65, 2014.
DOI : 10.1007/978-3-642-40193-0_3

URL : https://hal.archives-ouvertes.fr/hal-01588573

A. Carbone and L. Dib, Co-evolution and information signals in biological sequences, Theoretical Computer Science, vol.412, issue.23, pp.2486-2495, 2011.
DOI : 10.1016/j.tcs.2010.10.040

URL : https://hal.archives-ouvertes.fr/hal-01588981

R. Champeimont, E. Laine, S. W. Hu, F. Penin, and A. Carbone, Coevolution analysis of Hepatitis C virus genome to identify the structural and functional dependency network of viral proteins, Scientific Reports, vol.13, issue.1, p.26401, 2016.
DOI : 10.1186/1471-2105-13-194

URL : https://hal.archives-ouvertes.fr/hal-01320023

J. Changeux, The Feedback Control Mechanism of Biosynthetic L-Threonine Deaminase by L-Isoleucine, Cold Spring Harbor symposia on quantitative biology, pp.313-318, 1961.
DOI : 10.1101/SQB.1961.026.01.037

R. Chattopadhyaya, E. William, . Meador, R. Anthony, . Means et al., Calmodulin structure refined at 1.7 ?? resolution, Journal of Molecular Biology, vol.228, issue.4, pp.1177-1192, 1992.
DOI : 10.1016/0022-2836(92)90324-D

I. Chauvot-de-beauchene, A. Allain, N. Panel, E. Laine, A. Trouve et al., Hotspot Mutations in KIT Receptor Differentially Modulate Its Allosterically Coupled Conformational Dynamics: Impact on Activation and Drug Sensitivity, PLoS Computational Biology, vol.378, issue.7, p.1003749, 2014.
DOI : 10.1371/journal.pcbi.1003749.s010

URL : https://hal.archives-ouvertes.fr/hal-01505833

H. Chen, J. Ma, W. Li, A. V. Eliseenkova, C. Xu et al., A Molecular Brake in the Kinase Hinge Region Regulates the Activity of Receptor Tyrosine Kinases, Molecular Cell, vol.27, issue.5, pp.27717-730, 2007.
DOI : 10.1016/j.molcel.2007.06.028

G. Cheng, B. Qian, R. Samudrala, and D. Baker, Improvement in protein functional site prediction by distinguishing structural and functional constraints on protein family evolution using computational design, Nucleic Acids Research, vol.33, issue.18, pp.5861-5867, 2005.
DOI : 10.1093/nar/gki894

J. Cheng, A. Randall, and P. Baldi, Prediction of protein stability changes for single-site mutations using support vector machines, Proteins: Structure, Function, and Bioinformatics, vol.22, issue.4, pp.1125-1132, 2006.
DOI : 10.1007/978-1-4757-2440-0

C. Chennubhotla and I. Bahar, Signal Propagation in Proteins and Relation to Equilibrium Fluctuations, PLoS Computational Biology, vol.6, issue.9, p.172, 2007.
DOI : 0006-2960(2004)043[9426:HPSAUS]2.0.CO;2

URL : http://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.0030172&type=printable

C. N. Chi, L. Elfstrom, Y. Shi, T. Snall, A. Engstrom et al., Reassessing a sparse energetic network within a single protein domain, Proceedings of the National Academy of Sciences, vol.116, issue.3, pp.4679-4684, 2008.
DOI : 10.1016/j.bpc.2005.04.006

URL : http://www.pnas.org/content/105/12/4679.full.pdf

F. Chiappori, I. Merelli, G. Colombo, L. Milanesi, and G. Morra, Molecular Mechanism of Allosteric Communication in Hsp70 Revealed by Molecular Dynamics Simulations, PLoS Computational Biology, vol.95, issue.12, pp.1002844-2012
DOI : 10.1371/journal.pcbi.1002844.s012

F. Marcio, . Colombo, C. Donald, A. Rau, and . Parsegian, Protein solvation in allosteric regulation: a water effect on hemoglobin, Science, issue.5057, p.256655, 1992.

G. Communie, T. Crépin, D. Maurin, M. Ringkjøbing-jensen, M. Blackledge et al., Structure of the Tetramerization Domain of Measles Virus Phosphoprotein, Journal of Virology, vol.87, issue.12, pp.7166-7169, 2013.
DOI : 10.1128/JVI.00487-13

URL : https://hal.archives-ouvertes.fr/hal-01321590

P. Mazure, L. Dessen, D. R. Tchertanov, W. Mole, P. Kaelin et al., Genetic evidence of a precisely tuned dysregulation in the hypoxia signaling pathway during oncogenesis, Cancer Res, vol.74, issue.22, pp.6554-6564, 2014.
URL : https://hal.archives-ouvertes.fr/inserm-01401701

P. Da-silva-figueiredo-celestino-gomes, N. Panel, E. Laine, P. G. Pascutti, E. Solary et al., Differential Effects of CSF-1R D802V and KIT D816V Homologous Mutations on Receptor Tertiary Structure and Allosteric Communication, PLoS ONE, vol.119, issue.5, p.97519, 2014.
DOI : 10.1371/journal.pone.0097519.s006

URL : https://hal.archives-ouvertes.fr/hal-01588567

T. Darden, D. York, and L. Pedersen, ) method for Ewald sums in large systems, The Journal of Chemical Physics, vol.9, issue.12, pp.10089-10092, 1993.
DOI : 10.1126/science.2548279

T. A. De-beer, K. Berka, J. M. Thornton, and R. A. Laskowski, PDBsum additions, Nucleic Acids Research, vol.42, issue.D1, pp.292-296, 2014.
DOI : 10.1093/nar/gkt940

F. David-de-juan, A. Pazos, and . Valencia, Emerging methods in protein co-evolution, Nature Reviews Genetics, vol.485, issue.4, pp.249-261, 2013.
DOI : 10.1371/journal.pgen.1000570

A. M. De-vos, M. Ultsch, and A. A. Kossiakoff, Human growth hormone and extracellular domain of its receptor: crystal structure of the complex, Science, vol.255, issue.5042, pp.255306-312, 1992.
DOI : 10.1126/science.1549776

Y. Dehouck, J. M. Kwasigroch, D. Gilis, and M. Rooman, PoPMuSiC 2.1: a web server for the estimation of protein stability changes upon mutation and sequence optimality, BMC Bioinformatics, vol.12, issue.1, p.151, 2011.
DOI : 10.1186/1471-2105-8-65

Y. Dehouck, D. Gilis, and M. Rooman, A New Generation of Statistical Potentials for Proteins, Biophysical Journal, vol.90, issue.11, pp.4010-4017, 2006.
DOI : 10.1529/biophysj.105.079434

A. Del-sol, H. Fujihashi, D. Amoros, and R. Nussinov, Residues crucial for maintaining short paths in network communication mediate signaling in proteins, Molecular systems biology, 2006.
DOI : 10.1093/oxfordjournals.molbev.a003957

A. Del-sol, M. J. Araúzo-bravo, D. Amoros, and R. Nussinov, Modular architecture of protein structures and allosteric communications: potential implications for signaling proteins and regulatory linkages, Genome Biology, vol.8, issue.5, 2007.
DOI : 10.1186/gb-2007-8-5-r92

L. Warren and . Delano, The pymol molecular graphics system, 2002.

X. Deng, J. Eickholt, and J. Cheng, A comprehensive overview of computational protein disorder prediction methods, Mol. BioSyst., vol.39, issue.suppl. 2, pp.114-121, 2012.
DOI : 10.1093/nar/gkr184

L. Dib and A. Carbone, CLAG: an unsupervised non hierarchical clustering algorithm handling biological data, BMC Bioinformatics, vol.13, issue.1, p.194, 2012.
DOI : 10.1007/s11222-008-9056-0

URL : https://hal.archives-ouvertes.fr/hal-01527271

L. Dib and A. Carbone, Protein Fragments: Functional and Structural Roles of Their Coevolution Networks, PLoS ONE, vol.52, issue.3, p.48124, 2012.
DOI : 10.1371/journal.pone.0048124.s019

URL : https://hal.archives-ouvertes.fr/hal-01527314

I. Ruxandra, D. Dima, and . Thirumalai, Determination of network of residues that regulate allostery in protein families using sequence analysis, Protein Science, vol.15, issue.2, pp.258-268, 2006.

A. Dixit and G. M. Verkhivker, Hierarchical Modeling of Activation Mechanisms in the ABL and EGFR Kinase Domains: Thermodynamic and Mechanistic Catalysts of Kinase Activation by Cancer Mutations, PLoS Computational Biology, vol.222, issue.8, p.1000487, 2009.
DOI : 10.1371/journal.pcbi.1000487.s011

A. Dixit, M. Gennady, and . Verkhivker, Computational Modeling of Allosteric Communication Reveals Organizing Principles of Mutation-Induced Signaling in ABL and EGFR Kinases, PLoS Computational Biology, vol.25, issue.10, p.1002179, 2011.
DOI : 10.1371/journal.pcbi.1002179.s006

Z. Dosztanyi, V. Csizmok, P. Tompa, and I. Simon, IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content, Bioinformatics, vol.21, issue.16, pp.3433-3434, 2005.
DOI : 10.1093/bioinformatics/bti541

Z. Dosztanyi, B. Meszaros, and I. Simon, ANCHOR: web server for predicting protein binding regions in disordered proteins, Bioinformatics, vol.25, issue.20, pp.2745-2746, 2009.
DOI : 10.1093/bioinformatics/btp518

URL : https://academic.oup.com/bioinformatics/article-pdf/25/20/2745/485325/btp518.pdf

D. A. Doyle, A. Lee, J. Lewis, E. Kim, M. Sheng et al., Crystal Structures of a Complexed and Peptide-Free Membrane Protein???Binding Domain: Molecular Basis of Peptide Recognition by PDZ, Cell, vol.85, issue.7, pp.1067-1076, 1996.
DOI : 10.1016/S0092-8674(00)81307-0

R. O. Dror, R. M. Dirks, J. P. Grossman, H. Xu, and D. E. Shaw, Biomolecular Simulation: A Computational Microscope for Molecular Biology, Annual Review of Biophysics, vol.41, issue.1, pp.429-452, 2012.
DOI : 10.1146/annurev-biophys-042910-155245

L. Chester, . Drum, J. Shui-zhong-yan, Y. Bard, D. Shen et al., Structural basis for the activation of anthrax adenylyl cyclase exotoxin by calmodulin, Nature, issue.6870, pp.415-396, 2002.

A. K. Dunker, J. D. Lawson, C. J. Brown, R. M. Williams, P. Romero et al., Intrinsically disordered protein, Journal of Molecular Graphics and Modelling, vol.19, issue.1, pp.26-59, 2001.
DOI : 10.1016/S1093-3263(00)00138-8

L. Duret and S. Abdeddaim, Multiple alignment for structural, functional, or phylogenetic analyses of homologous sequences, Bioinformatics: Sequence, Structure, and Databanks, pp.51-76, 2000.

C. E. Edling and B. Hallberg, c-Kit???A hematopoietic cell essential receptor tyrosine kinase, The International Journal of Biochemistry & Cell Biology, vol.39, issue.11, pp.1995-1998, 2007.
DOI : 10.1016/j.biocel.2006.12.005

S. Engelen, L. A. Trojan, S. Sacquin-mora, R. Lavery, and A. Carbone, Joint Evolutionary Trees: A Large-Scale Method To Predict Protein Interfaces Based on Sequence Sampling, PLoS Computational Biology, vol.13, issue.1, p.1000267, 2009.
DOI : 10.1371/journal.pcbi.1000267.s005

URL : https://hal.archives-ouvertes.fr/inserm-00705756

P. Daniel and . Faith, Conservation evaluation and phylogenetic diversity, Biological conservation, vol.61, issue.1, pp.1-10, 1992.

A. Mario, . Fares, A. Simon, and . Travers, A novel method for detecting intramolecular coevolution: adding a further dimension to selective constraints analyses, Genetics, vol.173, issue.1, pp.9-23, 2006.

M. Figliuzzi, H. Jacquier, A. Schug, O. Tenaillon, and M. Weigt, Coevolutionary Landscape Inference and the Context-Dependence of Mutations in Beta-Lactamase TEM-1, Molecular Biology and Evolution, vol.33, issue.1, pp.268-280, 2016.
DOI : 10.1093/molbev/msv211

URL : https://hal.archives-ouvertes.fr/hal-01284957

A. Fiser, R. K. , G. Do, and A. , Modeling of loops in protein structures, Protein Science, vol.14, issue.9, pp.1753-1773, 2000.
DOI : 10.1002/ijch.199400028

Z. H. Foda, Y. Shan, E. T. Kim, D. E. Shaw, and M. A. Seeliger, A dynamically coupled allosteric network underlies binding cooperativity in Src kinase, Nature Communications, vol.14, p.5939, 2015.
DOI : 10.1021/bi00045a027

URL : http://www.nature.com/articles/ncomms6939.pdf

D. M. Fowler and S. Fields, Deep mutational scanning: a new style of protein science, Nature Methods, vol.14, issue.8, pp.801-807, 2014.
DOI : 10.1093/bioinformatics/btr577

H. Frauenfelder, S. G. Sligar, and P. G. Wolynes, The energy landscapes and motions of proteins, Science, vol.254, issue.5038, pp.1598-1603, 1991.
DOI : 10.1126/science.1749933

K. Agya, . Frimpong, R. Rinat, . Abzalimov, N. Vladimir et al., Characterization of intrinsically disordered proteins with electrospray ionization mass spectrometry: Conformational heterogeneity of ?-synuclein, Proteins: Structure, Function, and Bioinformatics, vol.78, issue.3, pp.714-722, 2010.

J. Karl and . Fryxell, The coevolution of gene family trees, Trends in Genetics, vol.12, issue.9, pp.364-369, 1996.

K. S. Gajiwala, J. C. Wu, J. Christensen, G. D. Deshmukh, W. Diehl et al., KIT kinase mutants show unique mechanisms of drug resistance to imatinib and sunitinib in gastrointestinal stromal tumor patients, Proc. Natl. Acad. Sci. U.S.A, pp.1542-1547, 2009.
DOI : 10.1002/pro.5560061015

S. Gianni, S. R. Haq, L. C. Montemiglio, M. C. Jurgens, A. Engstrom et al., Sequence-specific Long Range Networks in PSD-95/Discs Large/ZO-1 (PDZ) Domains Tune Their Binding Selectivity, Journal of Biological Chemistry, vol.248, issue.31, pp.286-27167, 2011.
DOI : 10.1021/bi00089a032

URL : https://hal.archives-ouvertes.fr/pasteur-00982082

B. Gregory, . Gloor, C. Louise, . Martin, M. Lindi et al., Mutual information in protein multiple sequence alignments reveals two classes of coevolving positions, Biochemistry, pp.447156-7165, 2005.

C. Goh, A. Andrew, M. Bogan, D. Joachimiak, F. E. Walther et al., Co-evolution of proteins with their interaction partners 1 1Edited by B. Honig, Journal of Molecular Biology, vol.299, issue.2, pp.283-293, 2000.
DOI : 10.1006/jmbi.2000.3732

J. Griffith, J. Black, C. Faerman, L. Swenson, M. Wynn et al., The Structural Basis for Autoinhibition of FLT3 by the Juxtamembrane Domain, Molecular Cell, vol.13, issue.2, pp.169-178, 2004.
DOI : 10.1016/S1097-2765(03)00505-7

G. Harauz, V. Ladizhansky, and J. M. Boggs, Structural Polymorphism and Multifunctionality of Myelin Basic Protein, Biochemistry, vol.48, issue.34, pp.8094-8104, 2009.
DOI : 10.1021/bi901005f

URL : http://mcb.cbs.uoguelph.ca/people/faculty/publications/harauz-pub-27.pdf

B. He, K. Wang, Y. Liu, B. Xue, N. Vladimir et al., Predicting intrinsic disorder in proteins: an overview, Cell Research, vol.11, issue.8, pp.929-949, 2009.
DOI : 10.1186/1471-2105-10-8

URL : http://www.nature.com/cr/journal/v19/n8/pdf/cr200987a.pdf

K. Henzler-wildman and D. Kern, Dynamic personalities of proteins, Nature, vol.124, issue.7172, pp.964-972, 2007.
DOI : 10.1038/nature06522

URL : http://www.nature.com/nature/journal/v450/n7172/pdf/nature06522.pdf

N. Tjandra, H. Kuboniwa, . Hao-ren-stephan-grzesiek, A. Claude, and . Bax, Solution structure of calcium-free calmodulin, Nature structural biology, vol.2, issue.9, 1995.

M. Huse and J. Kuriyan, The Conformational Plasticity of Protein Kinases, Cell, vol.109, issue.3, pp.275-282, 2002.
DOI : 10.1016/S0092-8674(02)00741-9

M. Ikura and M. Clore, Solution structure of a calmodulin-target peptide complex by multidimensional NMR, Science, vol.256, issue.5057, p.632, 1992.
DOI : 10.1126/science.1585175

G. Invernizzi, M. Tiberti, M. Lambrughi, K. Lindorff-larsen, and E. Papaleo, Communication Routes in ARID Domains between Distal Residues in Helix 5 and the DNA-Binding Loops, PLoS Computational Biology, vol.52, issue.9, p.1003744, 2014.
DOI : 10.1371/journal.pcbi.1003744.s005

T. Ishida and K. Kinoshita, PrDOS: prediction of disordered protein regions from amino acid sequence, Nucleic Acids Research, vol.35, issue.Web Server, pp.460-464, 2007.
DOI : 10.1093/nar/gkm363

URL : https://academic.oup.com/nar/article-pdf/35/suppl_2/W460/9585500/gkm363.pdf

T. David, . Jones, W. Daniel, D. Buchan, M. Cozzetto et al., Psicov: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments, Bioinformatics, vol.28, issue.2, pp.184-190, 2012.

R. Roskoski-jr, Structure and regulation of Kit protein-tyrosine kinase???The stem cell factor receptor, Biochemical and Biophysical Research Communications, vol.338, issue.3, pp.1307-1315, 2005.
DOI : 10.1016/j.bbrc.2005.09.150

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 : 10.1016/0005-2795(73)90350-4

R. Kalescky, J. Liu, and P. Tao, Identifying Key Residues for Protein Allostery through Rigid Residue Scan, The Journal of Physical Chemistry A, vol.119, issue.9, pp.1689-1700, 2014.
DOI : 10.1021/jp5083455

B. Kamaraj and A. Bogaerts, Structure and Function of p53-DNA Complexes with Inactivation and Rescue Mutations: A Molecular Dynamics Simulation Study, PLOS ONE, vol.39, issue.8, p.134638, 2015.
DOI : 10.1371/journal.pone.0134638.s005

Y. Karami, E. Laine, and A. Carbone, Dissecting protein architecture with communication blocks and communicating segment pairs, BMC Bioinformatics, vol.42, issue.Database issue, p.13, 2016.
DOI : 10.1093/nar/gkt940

URL : https://hal.archives-ouvertes.fr/hal-01260475

D. Karlin, F. Ferron, B. Canard, and S. Longhi, Structural disorder and modular organization in Paramyxovirinae N and P, Journal of General Virology, vol.84, issue.12, pp.3239-3252, 2003.
DOI : 10.1099/vir.0.19451-0

URL : http://jgv.microbiologyresearch.org/deliver/fulltext/jgv/84/12/3239.pdf?itemId=/content/journal/jgv/10.1099/vir.0.19451-0&mimeType=pdf&isFastTrackArticle=

M. B. Kennedy, Origin of PDZ (DHR, GLGF) domains, Trends in Biochemical Sciences, vol.20, issue.9, p.350, 1995.
DOI : 10.1016/S0968-0004(00)89074-X

D. Kern, R. Erik, and . Zuiderweg, The role of dynamics in allosteric regulation, Current Opinion in Structural Biology, vol.13, issue.6, pp.748-757, 2003.
DOI : 10.1016/j.sbi.2003.10.008

G. Bostjan-kobe, R. Guncar, T. Buchholz, B. Huber, N. Maco et al., Crystallography and protein???protein interactions: biological interfaces and crystal contacts, Biochemical Society Transactions, vol.36, issue.6, pp.1438-1441, 2008.
DOI : 10.1042/BST0361438

J. Kuriyan, Allostery and Coupled Sequence Variation in Nuclear Hormone Receptors, Cell, vol.116, issue.3, pp.354-356, 2004.
DOI : 10.1016/S0092-8674(04)00125-4

URL : https://doi.org/10.1016/s0092-8674(04)00125-4

E. Laine, I. Chauvot-de-beauchene, D. Perahia, C. Auclair, and L. Tchertanov, Mutation D816V Alters the Internal Structure and Dynamics of c-KIT Receptor Cytoplasmic Region: Implications for Dimerization and Activation Mechanisms, PLoS Computational Biology, vol.36, issue.6, p.1002068, 2011.
DOI : 10.1371/journal.pcbi.1002068.s008

URL : https://hal.archives-ouvertes.fr/hal-01505755

E. Laine, I. Chauvot-de-beauchene, D. Perahia, C. Auclair, and L. Tchertanov, Mutation D816V Alters the Internal Structure and Dynamics of c-KIT Receptor Cytoplasmic Region: Implications for Dimerization and Activation Mechanisms, PLoS Computational Biology, vol.36, issue.6, p.1002068, 2011.
DOI : 10.1371/journal.pcbi.1002068.s008

URL : https://hal.archives-ouvertes.fr/hal-01505755

E. Laine, C. Auclair, and L. Tchertanov, Allosteric Communication across the Native and Mutated KIT Receptor Tyrosine Kinase, PLoS Computational Biology, vol.8, issue.8, p.2012
DOI : 10.1371/journal.pcbi.1002661.s003

URL : https://hal.archives-ouvertes.fr/hal-01588576

M. Landau, I. Mayrose, Y. Rosenberg, F. Glaser, E. Martz et al., ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures, Nucleic Acids Research, vol.33, issue.Web Server, pp.299-302, 2005.
DOI : 10.1093/nar/gki370

O. Lecompte, J. D. Thompson, F. Plewniak, J. Thierry, and O. Poch, Multiple alignment of complete sequences (MACS) in the post-genomic era, Gene, vol.270, issue.1-2, pp.17-30, 2001.
DOI : 10.1016/S0378-1119(01)00461-9

H. J. Lee and J. J. Zheng, PDZ domains and their binding partners: structure, specificity, and modification, Cell Communication and Signaling, vol.8, issue.1, 2010.
DOI : 10.1186/1478-811X-8-8

URL : http://doi.org/10.1186/1478-811x-8-8

H. Lei, C. Wu, Z. X. Wang, Y. Zhou, Y. Duan-lemmon et al., folding simulations, The Journal of Chemical Physics, vol.128, issue.23, pp.235105-1411117, 2008.
DOI : 10.1016/0021-9991(77)90098-5

T. Li, N. Kon, L. Jiang, M. Tan, T. Ludwig et al., Tumor Suppression in the Absence of p53-Mediated Cell-Cycle Arrest, Apoptosis, and Senescence, Cell, vol.149, issue.6, pp.1491269-1283, 2012.
DOI : 10.1016/j.cell.2012.04.026

L. Lian, NMR structural studies of glutathione S-transferase, Cellular and Molecular Life Sciences CMLS, vol.54, issue.4, pp.359-362, 1998.
DOI : 10.1007/s000180050164

O. Lichtarge and A. Wilkins, Evolution: a guide to perturb protein function and networks, Current Opinion in Structural Biology, vol.20, issue.3, pp.351-359, 2010.
DOI : 10.1016/j.sbi.2010.04.002

URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2916956/pdf

O. Lichtarge, H. R. Bourne, and F. E. Cohen, An Evolutionary Trace Method Defines Binding Surfaces Common to Protein Families, Journal of Molecular Biology, vol.257, issue.2, pp.342-358, 1996.
DOI : 10.1006/jmbi.1996.0167

URL : http://mammoth.bcm.tmc.edu/papers/lichtarge-2.1996.pdf

O. Lichtarge, E. Mathew, and . Sowa, Evolutionary predictions of binding surfaces and interactions, Current Opinion in Structural Biology, vol.12, issue.1, pp.21-27, 2002.
DOI : 10.1016/S0959-440X(02)00284-1

R. C. Liddington, Anthrax: A molecular full nelson, Nature, vol.415, issue.6870, pp.415373-374, 2002.
DOI : 10.1038/415373a

J. Liu and R. Nussinov, Allosteric effects in the marginally stable von Hippel-Lindau tumor suppressor protein and allostery-based rescue mutant design, Proceedings of the National Academy of Sciences, vol.112, issue.3, pp.901-906, 2008.
DOI : 10.1021/ja00172a038

W. Steve, R. Lockless, and . Ranganathan, Evolutionarily conserved pathways of energetic connectivity in protein families, Science, vol.286, issue.5438, pp.295-299, 1999.

J. Richard, . Loncharich, R. Bernard, . Brooks, W. Richard et al., Langevin dynamics of peptides: The frictional dependence of isomerization rates of n-acetylalanyl-N'methylamide, Biopolymers, vol.32, issue.5, pp.523-535, 1992.

S. Lu, H. Jang, R. Nussinov, and J. Zhang, The Structural Basis of Oncogenic Mutations G12, G13 and Q61 in Small GTPase K-Ras4B, Scientific Reports, vol.31, issue.1, p.21949, 2016.
DOI : 10.1021/acs.chemrev.5b00542

W. J. Lu, J. F. Amatruda, and J. M. Abrams, p53 ancestry: gazing through an evolutionary lens, Nature Reviews Cancer, vol.24, issue.10, pp.758-762, 2009.
DOI : 10.4161/auto.6730

S. Lukman, D. P. Lane, and C. S. Verma, Mapping the Structural and Dynamical Features of Multiple p53 DNA Binding Domains: Insights into Loop 1 Intrinsic Dynamics, PLoS ONE, vol.38, issue.11, p.80221, 2013.
DOI : 10.1371/journal.pone.0080221.s019

A. Lupas, M. Van-dyke, and J. Stock, Predicting coiled coils from protein sequences, Science, vol.252, issue.5009, pp.1162-1164, 1991.
DOI : 10.1126/science.252.5009.1162

E. Lyman and D. M. Zuckerman, Ensemble-Based Convergence Analysis of Biomolecular Trajectories, Biophysical Journal, vol.91, issue.1, pp.164-172, 2006.
DOI : 10.1529/biophysj.106.082941

URL : https://doi.org/10.1529/biophysj.106.082941

M. A. Marti-renom, A. C. Stuart, A. Fiser, R. Sanchez, F. Melo et al., Comparative Protein Structure Modeling of Genes and Genomes, Annual Review of Biophysics and Biomolecular Structure, vol.29, issue.1, pp.291-325, 2000.
DOI : 10.1146/annurev.biophys.29.1.291

J. Andrew-mccammon, R. Bruce, M. Gelin, and . Karplus, Dynamics of folded proteins, Nature, vol.58, issue.5612, pp.585-590, 1977.
DOI : 10.1038/267585a0

C. L. Mcclendon, A. P. Kornev, M. K. Gilson, and S. S. Taylor, Dynamic architecture of a protein kinase, Proceedings of the National Academy of Sciences, pp.4623-4631, 2014.
DOI : 10.1073/pnas.1111471108

I. K. Mcdonald and J. M. Thornton, Satisfying Hydrogen Bonding Potential in Proteins, Journal of Molecular Biology, vol.238, issue.5, pp.777-793, 1994.
DOI : 10.1006/jmbi.1994.1334

. Pande, Mdtraj: a modern, open library for the analysis of molecular dynamics trajectories

R. N. Mclaughlin, F. J. Poelwijk, A. Raman, W. S. Gosal, and R. Ranganathan, The spatial architecture of protein function and adaptation, Nature, vol.13, issue.7422, pp.491138-142, 2012.
DOI : 10.1016/S1097-2765(03)00483-0

R. Jr, J. Frank, A. Poelwijk, . Raman, S. Walraj et al., The spatial architecture of protein function and adaptation, Nature, issue.7422, pp.491138-142, 2012.

Y. Mei, M. Su, G. Soni, S. Salem, L. Christopher et al., Intrinsically disordered regions in autophagy proteins, Proteins: Structure, Function, and Bioinformatics, vol.14, issue.4, pp.565-578, 2014.
DOI : 10.1016/j.cbpa.2010.06.169

URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3949125/pdf

J. Lasota, M. Miettinen, and M. Majidi, Pathology and diagnostic criteria of gastrointestinal stromal tumors (gists): a review, Eur J Cancer, issue.5, pp.39-51, 2002.

I. Mihalek, I. Res, and O. Lichtarge, A Family of Evolution???Entropy Hybrid Methods for Ranking Protein Residues by Importance, Journal of Molecular Biology, vol.336, issue.5, pp.1265-1282, 2004.
DOI : 10.1016/j.jmb.2003.12.078

H. Mizutani, . Saraboji, . Sm-malathy-sony, . Mn-ponnuswamy, K. Kumarevel et al., Systematic study on crystal-contact engineering of diphthine synthase: influence of mutations at crystal-packing regions on X-ray diffraction quality, Acta Crystallographica Section D Biological Crystallography, vol.64, issue.10, pp.641020-1033, 2008.
DOI : 10.1107/S0907444908023019/mh5014sup1.pdf

J. Monod, J. Wyman, and J. P. Changeux, On the nature of allosteric transitions: A plausible model, Journal of Molecular Biology, vol.12, issue.1, pp.88-118, 1965.
DOI : 10.1016/S0022-2836(65)80285-6

J. Monod and F. Jacob, General conclusions: teleonomic mechanisms in cellular metabolism, growth, and differentiation, Cold Spring Harbor symposia on quantitative biology, pp.389-401, 1961.
DOI : 10.1101/sqb.1961.026.01.048

F. Morcos, A. Pagnani, B. Lunt, A. Bertolino, D. S. Marks et al., Direct-coupling analysis of residue coevolution captures native contacts across many protein families, Proceedings of the National Academy of Sciences, vol.9, issue.8, pp.1293-1301, 2011.
DOI : 10.1101/gad.1125603

URL : https://hal.archives-ouvertes.fr/hal-01589010

F. Morcos, B. Jana, T. Hwa, N. José, and . Onuchic, Coevolutionary signals across protein lineages help capture multiple protein conformations, Proceedings of the National Academy of Sciences, vol.38, issue.suppl_1, pp.20533-20538, 2013.
DOI : 10.1093/nar/gkp985

URL : http://www.pnas.org/content/110/51/20533.full.pdf

G. Morra, A. Genoni, and G. Colombo, Mechanisms of Differential Allosteric Modulation in Homologous Proteins: Insights from the Analysis of Internal Dynamics and Energetics of PDZ Domains, Journal of Chemical Theory and Computation, vol.10, issue.12, pp.5677-5689, 2014.
DOI : 10.1021/ct500326g

N. Hesam, . Motlagh, O. James, J. Wrabl, . Li et al., The ensemble nature of allostery, Nature, vol.508, issue.7496, pp.331-339, 2014.

J. Murciano-calles, C. Corbi-verge, M. Adela, I. Candel, . Luque et al., Post-Translational Modifications Modulate Ligand Recognition by the Third PDZ Domain of the MAGUK Protein PSD-95, PLoS ONE, vol.46, issue.2, p.2014
DOI : 10.1371/journal.pone.0090030.s003

P. C. Ng and S. Henikoff, SIFT: predicting amino acid changes that affect protein function, Nucleic Acids Research, vol.31, issue.13, pp.3812-3814, 2003.
DOI : 10.1093/nar/gkg509

URL : https://academic.oup.com/nar/article-pdf/31/13/3812/9487105/gkg509.pdf

B. Nolen, S. Taylor, and G. Ghosh, Regulation of Protein Kinases, Molecular Cell, vol.15, issue.5, pp.661-675, 2004.
DOI : 10.1016/j.molcel.2004.08.024

C. Notredame, Recent progress in multiple sequence alignment: a survey, Pharmacogenomics, vol.12, issue.6, pp.131-144, 2002.
DOI : 10.1002/prot.340170407

C. Notredame, Recent Evolutions of Multiple Sequence Alignment Algorithms, PLoS Computational Biology, vol.32, issue.8, p.123, 2007.
DOI : 0305-1048(2004)032[W606:CAWSFA]2.0.CO;2

URL : http://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.0030123&type=printable

A. L. Okorokov and E. V. Orlova, Structural biology of the p53 tumour suppressor, Current Opinion in Structural Biology, vol.19, issue.2, pp.197-202, 2009.
DOI : 10.1016/j.sbi.2009.02.003

A. Orfao, L. Garcia-montero, L. Sanchez, and . Escribano, Recent advances in the understanding of mastocytosis: the role of KIT mutations, British Journal of Haematology, vol.30, issue.1, pp.12-30, 2007.
DOI : 10.1073/pnas.97.14.7732

A. Pandini, A. Fornili, F. Fraternali, and J. Kleinjung, Gsatools: analysis of allosteric communication and functional local motions using a structural alphabet, Bioinformatics, issue.16, pp.292053-2055, 2013.

E. Papaleo, G. Renzetti, and M. Tiberti, Mechanisms of Intramolecular Communication in a Hyperthermophilic Acylaminoacyl Peptidase: A Molecular Dynamics Investigation, PLoS ONE, vol.25, issue.5, p.35686, 2012.
DOI : 10.1371/journal.pone.0035686.s009

F. Pazos and A. Valencia, Similarity of phylogenetic trees as indicator of protein???protein interaction, Protein Engineering, Design and Selection, vol.14, issue.9, pp.609-614, 2001.
DOI : 10.1093/protein/14.9.609

Z. Peng and L. Kurgan, Comprehensive Comparative Assessment of In-Silico Predictors of Disordered Regions, Current Protein & Peptide Science, vol.13, issue.1, pp.6-18, 2012.
DOI : 10.2174/138920312799277938

F. Max, L. Perutz, and . Teneyck, Stereochemistry of cooperative effects in hemoglobin, Cold Spring Harbor symposia on quantitative biology, pp.295-310, 1972.

F. Max, . Perutz, . Wilkinson, G. Paoli, and . Dodson, The stereochemical mechanism of the cooperative effects in hemoglobin revisited. Annual review of biophysics and biomolecular structure, pp.1-34, 1998.

V. Petkovic, M. Godi, A. V. Pandey, D. Lochmatter, C. R. Buchanan et al., Growth Hormone (GH) Deficiency Type II: A Novel GH-1 Gene Mutation (GH-R178H) Affecting Secretion and Action, The Journal of Clinical Endocrinology & Metabolism, vol.95, issue.2, pp.731-739, 2010.
DOI : 10.1210/jc.2009-1247

URL : https://academic.oup.com/jcem/article-pdf/95/2/731/9066647/jcem0731.pdf

S. Piana, L. John, . Klepeis, E. David, and . Shaw, Assessing the accuracy of physical models used in protein-folding simulations: quantitative evidence from long molecular dynamics simulations, Current Opinion in Structural Biology, vol.24, issue.0, pp.98-105, 2014.
DOI : 10.1016/j.sbi.2013.12.006

D. Pollock and W. Taylor, Effectiveness of correlation analysis in identifying protein residues undergoing correlated evolution, Protein Engineering Design and Selection, vol.10, issue.6, pp.647-657, 1997.
DOI : 10.1093/protein/10.6.647

T. Pupko, R. E. Bell, I. Mayrose, F. Glaser, and N. Ben, Rate4Site: an algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues, Bioinformatics, vol.18, issue.Suppl 1, pp.71-77, 2002.
DOI : 10.1093/bioinformatics/18.suppl_1.S71

F. Qiu, . Ray, P. Brown, . Barker, F. Jhanwar et al., Primary structure of c-kit: relationship with the csf-1/pdgf receptor kinase family?oncogenic activation of v-kit involves deletion of extracellular domain and c terminus, The EMBO Journal, vol.7, issue.4, pp.1003-1011, 1988.

A. Rahman, Correlations in the Motion of Atoms in Liquid Argon, Physical Review, vol.110, issue.2A, p.405, 1964.
DOI : 10.1103/PhysRev.110.999

F. Raimondi, A. Felline, M. Seeber, S. Mariani, and F. Fanelli, A Mixed Protein Structure Network and Elastic Network Model Approach to Predict the Structural Communication in Biomolecular Systems: The PDZ2 Domain from Tyrosine Phosphatase 1E As a Case Study, Journal of Chemical Theory and Computation, vol.9, issue.5, pp.2504-2518, 2013.
DOI : 10.1021/ct400096f

K. Arun, . Ramani, M. Edward, and . Marcotte, Exploiting the co-evolution of interacting proteins to discover interaction specificity, Journal of molecular biology, vol.327, issue.1, pp.273-284, 2003.

D. C. Ramsey, M. P. Scherrer, T. Zhou, and C. O. Wilke, The Relationship Between Relative Solvent Accessibility and Evolutionary Rate in Protein Evolution, Genetics, vol.188, issue.2, pp.479-488, 2011.
DOI : 10.1534/genetics.111.128025

I. Michael, K. Sadowski, . Maksimiak, R. William, and . Taylor, Direct correlation analysis improves fold recognition, Computational Biology and Chemistry, vol.35, issue.5, pp.323-332, 2011.

G. Saladino and F. L. Gervasio, Modeling the effect of pathogenic mutations on the conformational landscape of protein kinases, Current Opinion in Structural Biology, vol.37, pp.108-114, 2016.
DOI : 10.1016/j.sbi.2016.01.005

S. Sankararaman, B. Kolaczkowski, and K. Sjolander, INTREPID: a web server for prediction of functionally important residues by evolutionary analysis, Nucleic Acids Research, vol.37, issue.Web Server, pp.390-395, 2009.
DOI : 10.1093/nar/gkp339

S. Sato, T. L. Religa, V. Daggett, and A. R. Fersht, From The Cover: Testing protein-folding simulations by experiment: B domain of protein A, Proceedings of the National Academy of Sciences, vol.24, issue.24, pp.6952-6956, 2004.
DOI : 10.1107/S0021889891004399

S. Sato, T. L. Religa, and A. R. Fersht, ??-Analysis of the Folding of the B Domain of Protein A Using Multiple Optical Probes, Journal of Molecular Biology, vol.360, issue.4, pp.850-864, 2006.
DOI : 10.1016/j.jmb.2006.05.051

P. Travis, W. Schrank, . Bolen, J. Vincent, and . Hilser, Rational modulation of conformational fluctuations in adenylate kinase reveals a local unfolding mechanism for allostery and functional adaptation in proteins, Proceedings of the National Academy of Sciences of the United States of America, vol.106, issue.40, pp.16984-16989, 2009.

M. Seeber, A. Felline, F. Raimondi, S. Muff, R. Friedman et al., Wordom: A user-friendly program for the analysis of molecular structures, trajectories, and free energy surfaces, Journal of Computational Chemistry, vol.101, issue.Web Server issu, pp.1183-1194, 2011.
DOI : 10.1073/pnas.0406234101

J. David, . Sidote, W. David, and . Hoffman, Nmr structure of an archaeal homologue of ribonuclease p protein rpp29, Biochemistry, vol.42, issue.46, pp.13541-13550, 2003.

L. Skjaerven, X. Yao, G. Scarabelli, J. Barry, and . Grant, Integrating protein structural dynamics and evolutionary analysis with Bio3D, BMC Bioinformatics, vol.5, issue.1, p.399, 2014.
DOI : 10.1186/gb-2004-5-10-r80

C. A. Smith and T. Kortemme, Backrub-Like Backbone Simulation Recapitulates Natural Protein Conformational Variability and Improves Mutant Side-Chain Prediction, Journal of Molecular Biology, vol.380, issue.4, pp.742-756, 2008.
DOI : 10.1016/j.jmb.2008.05.023

URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2603262/pdf

J. Stetefeld, M. Jenny, T. Schulthess, R. Landwehr, J. Engel et al., Crystal structure of a naturally occurring parallel right-handed coiled coil tetramer, Nature Structural Biology, vol.7, issue.9, pp.772-776, 2000.
DOI : 10.1038/79006

H. Frank, A. Stillinger, and . Rahman, Improved simulation of liquid water by molecular dynamics, The Journal of Chemical Physics, vol.60, issue.4, pp.1545-1557, 1974.

A. Read and T. Strachan, Human Molecular Genetics, 1999.

M. Gürol, . Süel, W. Steve, . Lockless, A. Mark et al., Evolutionarily conserved networks of residues mediate allosteric communication in proteins, Nature Structural & Molecular Biology, vol.10, issue.1, pp.59-69, 2003.

M. Gürol, . Süel, W. Steve, . Lockless, A. Mark et al., Evolutionarily conserved networks of residues mediate allosteric communication in proteins, Nature Structural & Molecular Biology, vol.10, issue.1, pp.59-69, 2003.

M. Sundstrom, T. Lundqvist, J. Rodin, L. B. Giebel, D. Milligan et al., Crystal Structure of an Antagonist Mutant of Human Growth Hormone, G120R, in Complex with Its Receptor at 2.9 ?? Resolution, Journal of Biological Chemistry, vol.269, issue.50, pp.27132197-32203, 1996.
DOI : 10.1107/S0108270193012338

Y. M. Sung, A. D. Wilkins, G. J. Rodriguez, T. G. Wensel, and O. Lichtarge, Intramolecular allosteric communication in dopamine D2 receptor revealed by evolutionary amino acid covariation, Proceedings of the National Academy of Sciences, vol.14, issue.4, pp.3539-3544, 2016.
DOI : 10.1074/jbc.M114.574483

URL : http://www.pnas.org/content/113/13/3539.full.pdf

D. Julie, F. Thompson, O. Plewniak, and . Poch, A comprehensive comparison of multiple sequence alignment programs, Nucleic acids research, vol.27, issue.13, pp.2682-2690, 1999.

M. Tiberti, G. Invernizzi, M. Lambrughi, Y. Inbar, G. Schreiber et al., PyInteraph: A Framework for the Analysis of Interaction Networks in Structural Ensembles of Proteins, Journal of Chemical Information and Modeling, vol.54, issue.5, pp.1537-1551, 2014.
DOI : 10.1021/ci400639r

G. Tiwari and D. Mohanty, An In Silico Analysis of the Binding Modes and Binding Affinities of Small Molecule Modulators of PDZ-Peptide Interactions, PLoS ONE, vol.23, issue.8, p.2013
DOI : 10.1371/journal.pone.0071340.s007

C. Tsai, A. Del-sol, and R. Nussinov, Allostery: Absence of a Change in Shape Does Not Imply that Allostery Is Not at Play, Journal of Molecular Biology, vol.378, issue.1, pp.1-11, 2008.
DOI : 10.1016/j.jmb.2008.02.034

N. Vladimir, K. Uversky, and . Dunker, Understanding protein non-folding, BBA)-Proteins and Proteomics, pp.1231-1264, 2010.

S. W. Vetter and E. Leclerc, Novel aspects of calmodulin target recognition and activation, European Journal of Biochemistry, vol.268, issue.3, pp.404-414, 2003.
DOI : 10.1074/jbc.M004778200

URL : http://onlinelibrary.wiley.com/doi/10.1046/j.1432-1033.2003.03414.x/pdf

P. Hansia, S. Vishveshwara, and A. Ghosh, Intra and inter-molecular communications through protein structure network, Curr Protein Pept Sci, vol.10, issue.2, pp.146-60, 2009.

B. Vogelstein, D. Lane, and A. J. Levine, Surfing the p53 network, Nature, vol.7, issue.6810, pp.307-310, 2000.
DOI : 10.1007/BF02725338

K. H. Vousden and C. Prives, Blinded by the Light: The Growing Complexity of p53, Cell, vol.137, issue.3, pp.413-431, 2009.
DOI : 10.1016/j.cell.2009.04.037

E. Michael, . Wall, B. James, . Clarage, N. George et al., Motions of calmodulin characterized using both bragg and diffuse x-ray scattering, Structure, vol.5, issue.12, pp.1599-1612, 1997.

M. Iain, G. Wallace, . Blackshields, G. Desmond, and . Higgins, Multiple sequence alignments, Current opinion in structural biology, vol.15, issue.3, pp.261-266, 2005.

S. T. Walsh, J. E. Sylvester, and A. A. Kossiakoff, The high- and low-affinity receptor binding sites of growth hormone are allosterically coupled, Proceedings of the National Academy of Sciences, vol.43, issue.20, pp.17078-17083, 2004.
DOI : 10.1021/bi036069b

D. James, . Watson, A. Roman, J. M. Laskowski, and . Thornton, Predicting protein function from sequence and structural data, Current opinion in structural biology, vol.15, issue.3, pp.275-284, 2005.

G. Weber, Ligand binding and internal equilibiums in proteins, Biochemistry, vol.11, issue.5, pp.864-878, 1972.
DOI : 10.1021/bi00755a028

M. Weigt, R. A. White, H. Szurmant, J. A. Hoch, and T. Hwa, Identification of direct residue contacts in protein-protein interaction by message passing, Proceedings of the National Academy of Sciences, vol.36, issue.suppl_1, pp.67-72, 2009.
DOI : 10.1093/nar/gkm960

W. Wriggers, K. A. Stafford, Y. Shan, S. Piana, P. Maragakis et al., Automated Event Detection and Activity Monitoring in Long Molecular Dynamics Simulations, Journal of Chemical Theory and Computation, vol.5, issue.10, pp.2595-2605, 2009.
DOI : 10.1021/ct900229u

E. Peter, H. Wright, and . Dyson, Intrinsically unstructured proteins: re-assessing the protein structure-function paradigm, Journal of molecular biology, vol.293, issue.2, pp.321-331, 1999.

C. Yeang and D. Haussler, Detecting Coevolution in and among Protein Domains, PLoS Computational Biology, vol.31, issue.11, p.211, 2007.
DOI : 10.1371/journal.pcbi.0030211.st001

URL : http://doi.org/10.1371/journal.pcbi.0030211

Z. Zhang and W. Wriggers, Local feature analysis: A statistical theory for reproducible essential dynamics of large macromolecules, Proteins: Structure, Function, and Bioinformatics, vol.35, issue.8, pp.391-403, 2006.
DOI : 10.1007/978-94-015-7658-1_21