A method and server for predicting damaging missense mutations, Nat. Methods, vol.7, issue.4, pp.248-249, 2010. ,
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
Studies in molecular dynamics. i. general method, The Journal of Chemical Physics, vol.31, issue.2, pp.459-466, 1959. ,
Phase Transition for a Hard Sphere System, The Journal of Chemical Physics, vol.27, issue.5, p.1208, 1957. ,
DOI : 10.1063/1.1743956
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
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
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. ,
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
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
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
Molecular dynamics with coupling to an external bath, The Journal of chemical physics, issue.8, pp.813684-3690, 1984. ,
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
An automated approach to network features of protein structure ensembles, Protein Science, vol.22, issue.10, pp.1399-1416 ,
DOI : 10.1002/pro.2333
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
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
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
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
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
Network analysis of protein dynamics, FEBS Letters, vol.104, issue.15, pp.2776-2782, 2007. ,
DOI : 10.1073/pnas.0607132104
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
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
Evolution and disorder, Current opinion in structural biology, vol.21, issue.3, pp.441-446, 2011. ,
Crystal structure of the nipah virus phosphoprotein tetramerization domain, Journal of virology, vol.88, issue.1, pp.758-762, 2014. ,
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
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
-Dependent Misfolding of the p53 DNA Binding Domain, Biochemistry, vol.46, issue.10, pp.2630-2639, 2007. ,
DOI : 10.1021/bi062106y
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
Protein solvation in allosteric regulation: a water effect on hemoglobin, Science, issue.5057, p.256655, 1992. ,
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
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
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
) 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
PDBsum additions, Nucleic Acids Research, vol.42, issue.D1, pp.292-296, 2014. ,
DOI : 10.1093/nar/gkt940
Emerging methods in protein co-evolution, Nature Reviews Genetics, vol.485, issue.4, pp.249-261, 2013. ,
DOI : 10.1371/journal.pgen.1000570
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
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
A New Generation of Statistical Potentials for Proteins, Biophysical Journal, vol.90, issue.11, pp.4010-4017, 2006. ,
DOI : 10.1529/biophysj.105.079434
Residues crucial for maintaining short paths in network communication mediate signaling in proteins, Molecular systems biology, 2006. ,
DOI : 10.1093/oxfordjournals.molbev.a003957
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
The pymol molecular graphics system, 2002. ,
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
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
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
Determination of network of residues that regulate allostery in protein families using sequence analysis, Protein Science, vol.15, issue.2, pp.258-268, 2006. ,
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
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
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
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
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
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
Structural basis for the activation of anthrax adenylyl cyclase exotoxin by calmodulin, Nature, issue.6870, pp.415-396, 2002. ,
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
Multiple alignment for structural, functional, or phylogenetic analyses of homologous sequences, Bioinformatics: Sequence, Structure, and Databanks, pp.51-76, 2000. ,
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
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
Conservation evaluation and phylogenetic diversity, Biological conservation, vol.61, issue.1, pp.1-10, 1992. ,
A novel method for detecting intramolecular coevolution: adding a further dimension to selective constraints analyses, Genetics, vol.173, issue.1, pp.9-23, 2006. ,
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
Modeling of loops in protein structures, Protein Science, vol.14, issue.9, pp.1753-1773, 2000. ,
DOI : 10.1002/ijch.199400028
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
Deep mutational scanning: a new style of protein science, Nature Methods, vol.14, issue.8, pp.801-807, 2014. ,
DOI : 10.1093/bioinformatics/btr577
The energy landscapes and motions of proteins, Science, vol.254, issue.5038, pp.1598-1603, 1991. ,
DOI : 10.1126/science.1749933
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. ,
The coevolution of gene family trees, Trends in Genetics, vol.12, issue.9, pp.364-369, 1996. ,
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
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
Mutual information in protein multiple sequence alignments reveals two classes of coevolving positions, Biochemistry, pp.447156-7165, 2005. ,
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
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
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
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
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
Solution structure of calcium-free calmodulin, Nature structural biology, vol.2, issue.9, 1995. ,
The Conformational Plasticity of Protein Kinases, Cell, vol.109, issue.3, pp.275-282, 2002. ,
DOI : 10.1016/S0092-8674(02)00741-9
Solution structure of a calmodulin-target peptide complex by multidimensional NMR, Science, vol.256, issue.5057, p.632, 1992. ,
DOI : 10.1126/science.1585175
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
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
Psicov: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments, Bioinformatics, vol.28, issue.2, pp.184-190, 2012. ,
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
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
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
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
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
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=
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
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
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
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
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
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
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
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
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
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
folding simulations, The Journal of Chemical Physics, vol.128, issue.23, pp.235105-1411117, 2008. ,
DOI : 10.1016/0021-9991(77)90098-5
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
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
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
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
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
Anthrax: A molecular full nelson, Nature, vol.415, issue.6870, pp.415373-374, 2002. ,
DOI : 10.1038/415373a
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
Evolutionarily conserved pathways of energetic connectivity in protein families, Science, vol.286, issue.5438, pp.295-299, 1999. ,
Langevin dynamics of peptides: The frictional dependence of isomerization rates of n-acetylalanyl-N'methylamide, Biopolymers, vol.32, issue.5, pp.523-535, 1992. ,
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
p53 ancestry: gazing through an evolutionary lens, Nature Reviews Cancer, vol.24, issue.10, pp.758-762, 2009. ,
DOI : 10.4161/auto.6730
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
Predicting coiled coils from protein sequences, Science, vol.252, issue.5009, pp.1162-1164, 1991. ,
DOI : 10.1126/science.252.5009.1162
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
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
Dynamics of folded proteins, Nature, vol.58, issue.5612, pp.585-590, 1977. ,
DOI : 10.1038/267585a0
Dynamic architecture of a protein kinase, Proceedings of the National Academy of Sciences, pp.4623-4631, 2014. ,
DOI : 10.1073/pnas.1111471108
Satisfying Hydrogen Bonding Potential in Proteins, Journal of Molecular Biology, vol.238, issue.5, pp.777-793, 1994. ,
DOI : 10.1006/jmbi.1994.1334
Mdtraj: a modern, open library for the analysis of molecular dynamics trajectories ,
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
The spatial architecture of protein function and adaptation, Nature, issue.7422, pp.491138-142, 2012. ,
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
Pathology and diagnostic criteria of gastrointestinal stromal tumors (gists): a review, Eur J Cancer, issue.5, pp.39-51, 2002. ,
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
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
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
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
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
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
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
The ensemble nature of allostery, Nature, vol.508, issue.7496, pp.331-339, 2014. ,
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
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
Regulation of Protein Kinases, Molecular Cell, vol.15, issue.5, pp.661-675, 2004. ,
DOI : 10.1016/j.molcel.2004.08.024
Recent progress in multiple sequence alignment: a survey, Pharmacogenomics, vol.12, issue.6, pp.131-144, 2002. ,
DOI : 10.1002/prot.340170407
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
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
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
Gsatools: analysis of allosteric communication and functional local motions using a structural alphabet, Bioinformatics, issue.16, pp.292053-2055, 2013. ,
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
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
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
Stereochemistry of cooperative effects in hemoglobin, Cold Spring Harbor symposia on quantitative biology, pp.295-310, 1972. ,
The stereochemical mechanism of the cooperative effects in hemoglobin revisited. Annual review of biophysics and biomolecular structure, pp.1-34, 1998. ,
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
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
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
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
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. ,
Correlations in the Motion of Atoms in Liquid Argon, Physical Review, vol.110, issue.2A, p.405, 1964. ,
DOI : 10.1103/PhysRev.110.999
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
Exploiting the co-evolution of interacting proteins to discover interaction specificity, Journal of molecular biology, vol.327, issue.1, pp.273-284, 2003. ,
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
Direct correlation analysis improves fold recognition, Computational Biology and Chemistry, vol.35, issue.5, pp.323-332, 2011. ,
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
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
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
??-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
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. ,
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
Nmr structure of an archaeal homologue of ribonuclease p protein rpp29, Biochemistry, vol.42, issue.46, pp.13541-13550, 2003. ,
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
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
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
Improved simulation of liquid water by molecular dynamics, The Journal of Chemical Physics, vol.60, issue.4, pp.1545-1557, 1974. ,
Human Molecular Genetics, 1999. ,
Evolutionarily conserved networks of residues mediate allosteric communication in proteins, Nature Structural & Molecular Biology, vol.10, issue.1, pp.59-69, 2003. ,
Evolutionarily conserved networks of residues mediate allosteric communication in proteins, Nature Structural & Molecular Biology, vol.10, issue.1, pp.59-69, 2003. ,
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
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
A comprehensive comparison of multiple sequence alignment programs, Nucleic acids research, vol.27, issue.13, pp.2682-2690, 1999. ,
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
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
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
Understanding protein non-folding, BBA)-Proteins and Proteomics, pp.1231-1264, 2010. ,
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
Intra and inter-molecular communications through protein structure network, Curr Protein Pept Sci, vol.10, issue.2, pp.146-60, 2009. ,
Surfing the p53 network, Nature, vol.7, issue.6810, pp.307-310, 2000. ,
DOI : 10.1007/BF02725338
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
Motions of calmodulin characterized using both bragg and diffuse x-ray scattering, Structure, vol.5, issue.12, pp.1599-1612, 1997. ,
Multiple sequence alignments, Current opinion in structural biology, vol.15, issue.3, pp.261-266, 2005. ,
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
Predicting protein function from sequence and structural data, Current opinion in structural biology, vol.15, issue.3, pp.275-284, 2005. ,
Ligand binding and internal equilibiums in proteins, Biochemistry, vol.11, issue.5, pp.864-878, 1972. ,
DOI : 10.1021/bi00755a028
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
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
Intrinsically unstructured proteins: re-assessing the protein structure-function paradigm, Journal of molecular biology, vol.293, issue.2, pp.321-331, 1999. ,
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
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