D. Jeffreys, Aspirin : The Extraordinary Story of a Wonder Drug, 2010.

E. D. Zanders, Laying the Foundations : Drug Discovery from Antiquity to the Twenty-First Century, The Science and Business of Drug Discovery, 2011.

E. Gregori-puigjané, V. Setola, and J. Hert, Identifying mechanismof-action targets for drugs and probes, Proceedings of the National Academy of Sciences, vol.109, pp.11178-11183, 2012.

M. Schenone, V. Dan?ík, K. Bridget, . Wagner, A. Paul et al., Target identification and mechanism of action in chemical biology and drug discovery, Nature chemical biology, vol.9, issue.2, p.232, 2013.

A. Wadood, . Ahmed, and . Shah, In-silico drug design : An approach which revolutionarised the drug discovery process, OA drug design & delivery, vol.1, pp.3-7, 2013.

E. Laine, C. Goncalves, and J. C. Karst, Use of allostery to identify inhibitors of calmodulin-induced activation of Bacillus anthracis edema factor, Proceedings of the National Academy of Sciences of the United States of America, vol.107, p.157, 2010.
URL : https://hal.archives-ouvertes.fr/pasteur-01501815

A. Berneman, L. Montout, and S. Goyard, Combined approaches for drug design points the way to novel proline racemase inhibitor candidates to fight Chagas disease, PLoS One, vol.8, 2013.
URL : https://hal.archives-ouvertes.fr/hal-00833388

A. Partricia-de, D. Amaral, G. Autheman, and . Dias-de-melo, Designed mono-and di-covalent inhibitors trap modeled functional motions for Trypanosoma cruzi proline racemase in crystallography, PLOS Neglected Tropical Diseases, 2018.

N. Desdouits, M. Nilges, and A. Blondel, Principal Component Analysis Reveals Correlation of Cavities Evolutionand Functional Motions in Proteins, Journal of Molecular Graphics and Modelling (oct. 2015) (cf. p. 3, 87, 96, 97, vol.129, p.167

J. Changeux, The nicotinic acetylcholine receptor : the founding father of the pentameric ligand-gated ion channel superfamily, Journal of Biological Chemistry, vol.287, issue.5, pp.40207-40215, 2012.

. Jp-changeux, M. Kasai, . Huchet, and . Meunier, Extraction from electric tissue of gymnotus of a protein presenting several typical properties characteristic of the physiological receptor of acetylcholine, Comptes rendus hebdomadaires des seances de l'Academie des sciences. Serie D : Sciences naturelles, vol.270, issue.7, p.2864, 1970.

. Bibliographie,

C. Neil-s-millar and . Gotti, Diversity of vertebrate nicotinic acetylcholine receptors, Neuropharmacology, vol.56, p.7, 2009.

N. Le-novere and J. Changeux, Molecular evolution of the nicotinic acetylcholine receptor : an example of multigene family in excitable cells, Journal of Molecular Evolution, vol.40, issue.7, pp.155-172, 1995.

. Wessler and . Kirkpatrick, Acetylcholine beyond neurons : the non-neuronal cholinergic system in humans, British journal of pharmacology, vol.154, issue.8, pp.1558-1571, 2008.

C. Léna, A. De-kerchove-d-exaerde, and M. Cordero-erausquin, Diversity and distribution of nicotinic acetylcholine receptors in the locus ceruleus neurons, Proceedings of the National Academy of Sciences 96, vol.21, pp.12126-12131, 1999.

A. J. Michael-w-quick-et-robin and . Lester, Desensitization of neuronal nicotinic receptors, Journal of neurobiology, vol.53, issue.8, pp.457-478, 2002.

, Nicotinic ACh Receptors Scientific Review, vol.132, p.8

S. Leonard, C. Adams, and . Charles-r-breese, Nicotinic receptor function in schizophrenia, Schizophrenia bulletin, vol.22, pp.431-446, 1996.

L. Tanya, D. Wallace, and . Bertrand, Alpha7 neuronal nicotinic receptors as a drug target in schizophrenia, Expert opinion on therapeutic targets, vol.17, pp.139-155, 2013.

C. Soler-alfonso, C. M. Carvalho, and J. Ge, CHRNA7 triplication associated with cognitive impairment and neuropsychiatric phenotypes in a threegeneration pedigree, European Journal of Human Genetics, vol.22, issue.8, p.1071, 2014.

A. Rozycka, J. Dorszewska, and B. Steinborn, A transcript coding for a partially duplicated form of ?7 nicotinic acetylcholine receptor is absent from the CD4+ T-lymphocytes of patients with autosomal dominant nocturnal frontal lobe epilepsy (ADNFLE), Folia neuropathologica, vol.51, pp.65-75, 2013.

H. Coon, M. E. Villalobos, and R. J. Robison, Genome-wide linkage using the Social Responsiveness Scale in Utah autism pedigrees, Molecular autism, vol.1, p.8, 2010.

M. Quik, D. Zhang, M. Mcgregor, and T. Bordia, Alpha7 nicotinic receptors as therapeutic targets for Parkinson's disease, Biochemical pharmacology 97, vol.4, pp.399-407, 2015.

R. Michael, G. Robert, and . Nagele, Targeting the alpha 7 nicotinic acetylcholine receptor to reduce amyloid accumulation in Alzheimer's disease pyramidal neurons, Current pharmaceutical design, vol.12, issue.6, pp.677-684, 2006.

M. Oz, G. Petroianu, E. Dietrich, and . Lorke, ?7-nicotinic acetylcholine receptors : new therapeutic avenues in Alzheimer s disease, Nicotinic Acetylcholine Receptor Technologies, pp.149-169, 2016.

Y. Ren-chao, J. Tong, Z. Li, Y. Lu, and . Yao, The protective effect of alpha 7 nicotinic acetylcholine receptor activation on critical illness and its mechanism, International journal of biological sciences, vol.13, issue.1, p.46, 2017.

K. Lawrence, . Leung, M. Francis, . Patafio, W. Walter et al., Gastrointestinal adverse effects of varenicline at maintenance dose : a meta-analysis, BMC clinical pharmacology, vol.11, issue.1, p.15, 2011.

Y. Muhamad, J. O. Elrashidi, and . Ebbert, Emerging drugs for the treatment of tobacco dependence : 2014 update, Expert opinion on emerging drugs, vol.19, issue.8, pp.243-260, 2014.

J. Cartaud, L. Benedetti, J. B. Cohen, J. Meunier, and J. Changeux, Presence of a lattice structure in membrane fragments rich in nicotinic receptor protein from the electric organ of Torpedo marmorata, FEBS letters, vol.33, p.9, 1973.

F. Hucho, Molecular weight and quaternary structure of the cholinergic receptor protein extracted by detergents from Electrophorus electricus electric tissue, FEBS letters, vol.38, p.9, 1973.

L. Cheryl, . Weill, G. Mark, A. Mcnamee, and . Karlin, Affinity-labeling of purified acetylcholine receptor from Torpedo californica, Biochemical and biophysical research communications, vol.61, p.9, 1974.

. Ma-raftery, . Vandlen, and . Michaelson, The biochemistry of an acetylcholine receptor, Journal of supramolecular structure, vol.2, p.9, 1974.

N. Unwin, Refined structure of the nicotinic acetylcholine receptor at 4 Å resolution, Journal of molecular biology, vol.346, p.11, 2005.

L. Claudio, C. M. Morales-perez, . Noviello, E. Ryan, and . Hibbs, X-ray structure of the human ?4?2 nicotinic receptor, Nature, vol.538, p.9, 2016.

S. Li, S. Huang, and N. Bren, Ligand-binding domain of an ? 7-nicotinic receptor chimera and its complex with agonist, Nature neuroscience, vol.14, p.135, 2011.

R. Spurny, S. Debaveye, and A. Farinha, Molecular blueprint of allosteric binding sites in a homologue of the agonist-binding domain of the ?7 nicotinic acetylcholine receptor, Proceedings of the National Academy of Sciences, vol.112, p.156, 2015.

X. Xiu, L. Nyssa, . Puskar, A. P. Jai, . Shanata et al., Nicotine binding to brain receptors requires a strong cation-? interaction, Nature, vol.458, p.133, 2009.

O. Beckstein, S. P. Mark, and . Sansom, A hydrophobic gate in an ion channel : the closed state of the nicotinic acetylcholine receptor, Physical biology, vol.3, issue.2, p.9, 2006.

. Bibliographie,

N. Le-novere, P. Corringer, and J. Changeux, The diversity of subunit composition in nAChRs : evolutionary origins, physiologic and pharmacologic consequences, Journal of neurobiology, vol.53, p.11, 2002.
URL : https://hal.archives-ouvertes.fr/pasteur-01719571

. S-kracun, . Harkness, . Gibb, and . Millar, Influence of the M3-M4 intracellular domain upon nicotinic acetylcholine receptor assembly, targeting and function, British journal of pharmacology, vol.153, p.11, 2008.

N. Kouvatsos, A. Niarchos, and P. Zisimopoulou, Purification and functional characterization of a truncated human ?4?2 nicotinic acetylcholine receptor, International journal of biological macromolecules, vol.70, p.11, 2014.

L. Sauguet, A. Shahsavar, and F. Poitevin, Crystal structures of a pentameric ligand-gated ion channel provide a mechanism for activation, Proceedings of the National Academy of Sciences, vol.111, p.42, 2014.
URL : https://hal.archives-ouvertes.fr/pasteur-01721583

E. Ryan-e-hibbs and . Gouaux, Principles of activation and permeation in an anionselective Cys-loop receptor, Nature, vol.474, p.156, 2011.

T. Althoff, E. Ryan, S. Hibbs, E. Banerjee, and . Gouaux, X-ray structures of GluCl in apo states reveal a gating mechanism of Cys-loop receptors, Nature, vol.512, p.42, 2014.

J. Du, W. Lü, S. Wu, Y. Cheng, and E. Gouaux, Glycine receptor mechanism elucidated by electron cryo-microscopy, Nature, vol.526, p.147, 2015.

S. Marie, L. Prevost, H. Sauguet, and . Nury, A locally closed conformation of a bacterial pentameric proton-gated ion channel, Nature structural & molecular biology, vol.19, issue.6, p.11, 2012.

J. Changeux, The nicotinic acetylcholine receptor : a typical 'allosteric machine, Phil. Trans. R. Soc. B, vol.373, p.11, 2018.

A. Taly, M. Delarue, and T. Grutter, Normal mode analysis suggests a quaternary twist model for the nicotinic receptor gating mechanism, Biophysical journal, vol.88, p.11, 2005.
URL : https://hal.archives-ouvertes.fr/pasteur-00162514

X. Cheng, B. Lu, B. Grant, J. Richard, . Law et al., Channel opening motion of ?7 nicotinic acetylcholine receptor as suggested by normal mode analysis, Journal of molecular biology, vol.355, issue.2, p.11, 2006.

H. Nury, F. Poitevin, and C. Van-renterghem, One-microsecond molecular dynamics simulation of channel gating in a nicotinic receptor homologue, Proceedings of the National Academy of Sciences, vol.107, p.48, 2010.
URL : https://hal.archives-ouvertes.fr/pasteur-02174737

S. Nicolas-e-martin, N. Malik, J. Calimet, M. Changeux, and . Cecchini, Un-gating and allosteric modulation of a pentameric ligand-gated ion channel captured by molecular dynamics, PLoS computational biology, vol.13, p.11, 2017.

C. Chothia, M. Arthur, and . Lesk, The relation between the divergence of sequence and structure in proteins, In : The EMBO journal, vol.5, p.12, 1986.

. Stephen-f-altschul, L. Thomas, A. A. Madden, and . Schäffer, Gapped BLAST and PSI-BLAST : a new generation of protein database search programs, Nucleic acids research, vol.25, p.12, 1997.

M. Helen, J. Berman, Z. Westbrook, and . Feng, The protein data bank, Nucleic acids research, vol.28, p.12, 2000.

C. Robert and . Edgar, MUSCLE : multiple sequence alignment with high accuracy and high throughput, Nucleic acids research, vol.32, p.12, 2004.

C. Notredame, G. Desmond, J. Higgins, and . Heringa, T-coffee : a novel method for fast and accurate multiple sequence alignment1, Journal of molecular biology, vol.302, p.12, 2000.

B. Webb and A. Sali, Comparative protein structure modeling using MODELLER, Current protocols in protein science, vol.86, p.13, 2016.

M. Shen and A. Sali, Statistical potential for assessment and prediction of protein structures, Protein science, vol.15, p.13, 2006.

F. Melo, R. Sánchez, and A. Sali, Statistical potentials for fold assessment, Protein science, vol.11, p.13, 2002.

A. Ray, E. Lindahl, and B. Wallner, Model quality assessment for membrane proteins, Bioinformatics, vol.26, p.13, 2010.

A. Jr, D. Bashford, and . Bellott, All-atom empirical potential for molecular modeling and dynamics studies of proteins, The journal of physical chemistry B, vol.102, p.54, 1998.

B. Robert, X. Best, J. Zhu, and . Shim, Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone ?, ? and side-chain ?1 and ?2 dihedral angles, Journal of chemical theory and computation, vol.8, issue.9, p.54, 2012.

A. Jr, M. Feig, L. Charles, and . Brooks, Improved treatment of the protein backbone in empirical force fields, Journal of the American Chemical Society, vol.126, p.16, 2003.

R. Bernard, . Brooks, L. Charles, A. D. Brooks, and . Mackerell, CHARMM : the biomolecular simulation program, Journal of computational chemistry, vol.30, p.16, 2009.

N. Schmid, A. P. Eichenberger, and A. Choutko, Definition and testing of the GROMOS force-field versions 54A7 and 54B7, European biophysics journal, vol.40, p.16, 2011.

A. David, T. E. Case, T. Cheatham, and . Darden, The Amber biomolecular simulation programs, Journal of computational chemistry, vol.26, p.16, 2005.

P. Paul and . Ewald, Die Berechnung optischer und elektrostatischer Gitterpotentiale, Annalen der physik, vol.369, p.16, 1921.

. Bibliographie,

U. Essmann, L. Perera, and M. L. Berkowitz, A smooth particle mesh Ewald method, The Journal of chemical physics, vol.103, p.16, 1995.

M. Schaefer and M. Karplus, A comprehensive analytical treatment of continuum electrostatics, The Journal of Physical Chemistry, vol.100, p.16, 1996.

R. Constanciel and R. Contreras, Self consistent field theory of solvent effects representation by continuum models : Introduction of desolvation contribution, Theoretica chimica acta, vol.65, p.16, 1984.

J. N. Joseph-d-bryngelson, . Onuchic, D. Nicholas, . Socci, G. Peter et al., Funnels, pathways, and the energy landscape of protein folding : a synthesis, Proteins : Structure, Function, and Bioinformatics, vol.21, p.17, 1995.

. Christian-b-anfinsen, Principles that govern the folding of protein chains, Science 181, vol.4096, p.17, 1973.

A. Laio and M. Parrinello, Escaping free-energy minima, Proceedings of the National Academy of Sciences, vol.99, p.19, 2002.

. Glenn-m-torrie, P. John, and . Valleau, Nonphysical sampling distributions in Monte Carlo free-energy estimation : Umbrella sampling, Journal of Computational Physics, vol.23, p.19, 1977.

J. Changeux, M. Kasai, and C. Lee, Use of a snake venom toxin to characterize the cholinergic receptor protein, Proceedings of the National Academy of Sciences, vol.67, p.22, 1970.

H. Cheng, C. Fan, and S. Zhang, Crystallization scale purification of ?7 nicotinic acetylcholine receptor from mammalian cells using a BacMam expression system, Acta Pharmacologica Sinica, vol.36, p.22, 2015.

E. John, S. E. Baenziger, . Ryan, M. Michael, and . Goodreid, Lipid composition alters drug action at the nicotinic acetylcholine receptor, Molecular pharmacology, vol.73, p.22, 2008.

T. Gareth, R. Young, A. S. Zwart, E. Walker, . Sher et al., Potentiation of ?7 nicotinic acetylcholine receptors via an allosteric transmembrane site, Proceedings of the National Academy of Sciences 105, vol.38, p.159, 2008.

J. Allison-domville, Mapping the Allosteric Pathway Leading from a Mutation in the Nicotinic Acetylcholine Receptor to a Congenital Myasthenic Syndrome, p.22, 2017.

J. Newcombe, A. Chatzidaki, D. Tom, M. Sheppard, . Topf et al., Diversity of nicotinic acetylcholine receptor positive allosteric modulators revealed by mutagenesis and a revised structural model, Molecular pharmacology, vol.40, p.156, 2017.

G. Richard-w-olsen, M. Li, and . Wallner, Structural models of ligandgated ion channels : sites of action for anesthetics and ethanol, Alcoholism : Clinical and Experimental Research, vol.38, p.22, 2014.

O. Megan, B. Mara, M. Cromer, S. Parker, and . Chung, Homology model of the GABA A receptor examined using Brownian dynamics, Biophysical journal, vol.88, p.22, 2005.

M. Luis, J. Valor, F. Mulet, and . Sala, Role of the large cytoplasmic loop of the ?7 neuronal nicotinic acetylcholine receptor subunit in receptor expression and function, Biochemistry 41, vol.25, p.25, 2002.

T. Madden, The BLAST sequence analysis tool, p.26, 2013.

Á. Nemecz and P. Taylor, Creating an ?7 Nicotinic Acetylcholine Recognition Domain from the Acetylcholine-binding Protein CRYSTALLOGRAPHIC AND LIGAND SELECTIVITY ANALYSES, Journal of Biological Chemistry, vol.286, p.26, 2011.

G. Hassaine, C. Deluz, and L. Grasso, X-ray structure of the mouse serotonin 5-HT 3 receptor, Nature, vol.512, p.27, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01102530

L. Chen, Y. Dellisanti, C. J. Yao, . Stroud, and . Wang, Crystal structure of the extracellular domain of nAChRa1 bound to alpha-bungarotoxin at 1.94 Å resolution, Nature Neurosci, vol.10, p.27, 2007.

M. Zouridakis, P. Giastas, and E. Zarkadas, Crystal structures of free and antagonist-bound states of human ?9 nicotinic receptor extracellular domain, Nature Structural and Molecular Biology, vol.21, p.27, 2014.

A. Bhattacharyya, On a measure of divergence between two statistical populations defined by their probability distributions, Bull. Calcutta Math. Soc, vol.35, p.30, 1943.

J. Sarel, A. Fleishman, J. E. Leaver-fay, and . Corn, RosettaScripts : a scripting language interface to the Rosetta macromolecular modeling suite, PloS one 6, vol.6, p.31, 2011.

D. Michael, . Tyka, A. Daniel, I. Keedy, and . André, Alternate states of proteins revealed by detailed energy landscape mapping, Journal of molecular biology, vol.405, p.31, 2011.

P. Barth, J. Schonbrun, and D. Baker, Toward high-resolution prediction and design of transmembrane helical protein structures, Proceedings of the National Academy of Sciences, vol.35, p.31, 2007.

C. E. Carol-a-rohl, . Strauss, M. S. Kira, D. Misura, and . Baker, Protein structure prediction using Rosetta, Methods in enzymology. T. 383, p.31, 2004.

C. Konstantinos-d-tsirigos, N. Peters, L. Shu, A. Käll, and . Elofsson, The TOPCONS web server for consensus prediction of membrane protein topology and signal peptides, Nucleic acids research 43, vol.1, p.31, 2015.

E. Baris, Y. Suzek, H. Wang, and . Huang, UniRef clusters : a comprehensive and scalable alternative for improving sequence similarity searches, Bioinformatics, vol.31, p.31, 2014.

. Bibliographie,

A. Roman, . Laskowski, W. Malcolm, D. Macarthur, . Moss et al., PROCHECK : a program to check the stereochemical quality of protein structures, Journal of applied crystallography, vol.26, p.31, 1993.

P. Benkert, M. Biasini, and T. Schwede, Toward the estimation of the absolute quality of individual protein structure models, Bioinformatics, vol.27, p.31, 2010.

. Vincent-b-chen, J. J. Bryan-arendall, and . Headd, MolProbity : all-atom structure validation for macromolecular crystallography, Acta Crystallographica Section D : Biological Crystallography, vol.66, issue.1, p.31, 2010.

D. Eisenberg, R. Lüthy, U. James, and . Bowie, 20] VERIFY3D : Assessment of protein models with three-dimensional profiles, Methods in enzymology. T. 277, p.31, 1997.

M. Wiederstein, J. Manfred, and . Sippl, ProSA-web : interactive web service for the recognition of errors in three-dimensional structures of proteins, Nucleic acids research, vol.35, p.31, 2007.

N. Unwin and Y. Fujiyoshi, Gating movement of acetylcholine receptor caught by plunge-freezing, Journal of molecular biology, vol.422, p.40, 2012.

N. Mnatsakanyan and M. Jansen, Experimental determination of the vertical alignment between the second and third transmembrane segments of muscle nicotinic acetylcholine receptors, Journal of neurochemistry, vol.125, p.40, 2013.

P. Corringer, M. Baaden, and N. Bocquet, Atomic structure and dynamics of pentameric ligand-gated ion channels : new insight from bacterial homologues, The Journal of physiology, vol.588, p.40, 2010.
URL : https://hal.archives-ouvertes.fr/pasteur-02174745

S. Paul, . Miller, and . Radu-aricescu, Crystal structure of a human GABA A receptor, Nature, vol.512, p.40, 2014.

M. Cecchini and J. Changeux, The nicotinic acetylcholine receptor and its prokaryotic homologues : Structure, conformational transitions & allosteric modulation, Neuropharmacology, vol.96, p.41, 2015.

K. Kaczanowska, M. Harel, and Z. Radi?, Structural basis for cooperative interactions of substituted 2-aminopyrimidines with the acetylcholine binding protein, Proceedings of the National Academy of Sciences, vol.72, p.42, 2014.

D. Liu, Y. Xu, and Y. Feng, Inhibitor discovery targeting the intermediate structure of ?-amyloid peptide on the conformational transition pathway : implications in the aggregation mechanism of ?-amyloid peptide, Biochemistry 45, vol.36, p.47, 2006.

E. Laine, D. Julliane, A. Yoneda, . Blondel, E. Thérese et al., The conformational plasticity of calmodulin upon calcium complexation gives a model of its interaction with the oedema factor of Bacillus anthracis, Proteins : Structure, Function, and Bioinformatics, vol.71, p.97, 2008.

W. Gan, S. Yang, and B. Roux, Atomistic view of the conformational activation of Src kinase using the string method with swarms-of-trajectories, Biophysical journal, vol.97, p.49, 2009.

D. Albert-c-pan, B. Sezer, and . Roux, Finding transition pathways using the string method with swarms of trajectories, The journal of physical chemistry B, vol.112, p.65, 2008.

M. Nina, . Goodey, J. Stephen, and . Benkovic, Allosteric regulation and catalysis emerge via a common route, Nature chemical biology, vol.4, p.48, 2008.

E. Rani-p-venkitakrishnan, D. Zaborowski, and . Mcelheny, Conformational changes in the active site loops of dihydrofolate reductase during the catalytic cycle, Biochemistry 43, vol.51, p.48, 2004.

R. Nussinov, C. Tsai, and B. Ma, The underappreciated role of allostery in the cellular network, Annual review of biophysics, vol.42, p.48, 2013.

D. Kern, R. P. Erik, and . Zuiderweg, The role of dynamics in allosteric regulation, Current opinion in structural biology 13, vol.6, p.48, 2003.

A. , Allosteric Modulators : An Emerging Concept in Drug Discovery, p.48, 2015.

S. Lu, M. Ji, D. Ni, and J. Zhang, Discovery of hidden allosteric sites as novel targets for allosteric drug design, Drug discovery today, p.48, 2017.

C. Levinthal, How to Fold Graciously. Mossbauer Spectroscopy in Biological Systems, p.48, 1969.

M. Fischer, K. Brian, . Shoichet, S. James, and . Fraser, One crystal, two temperatures : cryocooling penalties alter ligand binding to transient protein sites, ChemBioChem 16, vol.11, p.48, 2015.

T. Szyperski, Room Temperature X-Ray Crystallography Reveals Conformational Heterogeneity of Engineered Proteins, Structure 25, vol.5, p.48, 2017.

B. Meyer and . Jackson, Spontaneous openings of the acetylcholine receptor channel, Proceedings of the National Academy of Sciences, vol.81, p.48, 1984.

C. Abrams and G. Bussi, Enhanced sampling in molecular dynamics using metadynamics, replica-exchange, and temperature-acceleration, In : Entropy, vol.16, p.48, 2013.

V. Spiwok, Z. Sucur, and P. Hosek, Enhanced sampling techniques in biomolecular simulations, Biotechnology advances, vol.33, p.48, 2015.

. Bibliographie,

G. John and . Kirkwood, Statistical mechanics of fluid mixtures, The Journal of Chemical Physics, vol.3, p.49, 1935.

J. Hénin and C. Chipot, Overcoming free energy barriers using unconstrained molecular dynamics simulations, The Journal of chemical physics, vol.121, p.49, 2004.

L. Maragliano and E. Vanden-eijnden, A temperature accelerated method for sampling free energy and determining reaction pathways in rare events simulations, Chemical physics letters, vol.426, issue.3, p.49, 2006.

G. Peter, D. Bolhuis, C. Chandler, . Dellago, L. Phillip et al., Transition path sampling : Throwing ropes over rough mountain passes, in the dark, Annual review of physical chemistry, vol.53, p.49, 2002.

V. Sergei, M. Krivov, and . Karplus, Hidden complexity of free energy surfaces for peptide (protein) folding, Proceedings of the National Academy of Sciences of the United States of America, vol.101, p.49, 2004.

L. Maragliano, A. Fischer, E. Vanden-eijnden, and G. Ciccotti, String method in collective variables : Minimum free energy paths and isocommittor surfaces, The Journal of chemical physics, vol.125, issue.2, p.49, 2006.

C. Zhao and S. Y. Noskov, The molecular mechanism of ion-dependent gating in secondary transporters, PLoS computational biology, vol.9, p.49, 2013.

A. Chamberlin, F. Qiu, Y. Wang, Y. Sergei, . Noskov et al., Mapping the gating and permeation pathways in the voltage-gated proton channel Hv1, Journal of molecular biology, vol.427, p.49, 2015.

V. Ovchinnikov, M. Karplus, and E. Vanden-eijnden, Free energy of conformational transition paths in biomolecules : The string method and its application to myosin VI, The Journal of chemical physics, vol.134, p.49, 2011.

J. Jérôme, S. A. Lacroix, L. Pless, and . Maragliano, Intermediate state trapping of a voltage sensor, The Journal of general physiology, vol.140, issue.6, p.49, 2012.

M. Sanchez-martinez, M. Field, and R. Crehuet, Enzymatic minimum free energy path calculations using swarms of trajectories, The Journal of Physical Chemistry B, vol.119, p.49, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01234052

F. Pontiggia, . Pachov, and . Clarkson, Free energy landscape of activation in a signalling protein at atomic resolution, Nature communications, vol.6, p.49, 2015.

Y. Matsunaga, H. Fujisaki, and T. Terada, Minimum free energy path of ligand-induced transition in adenylate kinase, PLoS computational biology, vol.8, issue.6, p.49, 2012.

A. Singharoy, C. Chipot, M. Moradi, and K. Schulten, Chemomechanical coupling in hexameric protein-protein interfaces harnesses energy within V-Type ATPases, Journal of the American Chemical Society, vol.139, p.49, 2016.

Y. Matsunaga, T. Yamane, and T. Terada, Energetics and conformational pathways of functional rotation in the multidrug transporter AcrB, vol.7, p.49, 2018.

A. Das, H. Rui, R. Nakamoto, and . Benoît-roux, Conformational transitions and alternating-access mechanism in the sarcoplasmic reticulum calcium pump, Journal of molecular biology, vol.429, p.49, 2017.

M. Moradi, G. Enkavi, and E. Tajkhorshid, Atomic-level characterization of transport cycle thermodynamics in the glycerol-3-phosphate : phosphate antiporter, Nature communications, vol.6, p.49, 2015.

F. Zhu and G. Hummer, Pore opening and closing of a pentameric ligand-gated ion channel, Proceedings of the National Academy of Sciences, vol.107, p.49, 2010.

B. Lev, S. Murail, and F. Poitevin, String method solution of the gating pathways for a pentameric ligand-gated ion channel, Proceedings of the National Academy of Sciences, vol.114, p.71, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01644525

Y. Meng, D. Shukla, B. Vijay-s-pande, and . Roux, Transition path theory analysis of c-Src kinase activation, Proceedings of the National Academy of Sciences, vol.113, p.49, 2016.

H. Jónsson, G. Mills, W. Karsten, and . Jacobsen, Nudged elastic band method for finding minimum energy paths of transitions, Classical and quantum dynamics in condensed phase simulations, p.50, 1998.

W. E-weinan, E. Ren, and . Vanden-eijnden, String method for the study of rare events, Physical Review B, vol.66, p.50, 2002.

W. E-weinan, E. Ren, and . Vanden-eijnden, Simplified and improved string method for computing the minimum energy paths in barrier-crossing events, Journal of Chemical Physics, vol.126, p.50, 2007.

S. Fischer and M. Karplus, Conjugate peak refinement : an algorithm for finding reaction paths and accurate transition states in systems with many degrees of freedom, Chemical physics letters, vol.194, p.50, 1992.

S. Fischer, B. Windshügel, D. Horak, C. Kenneth, . Holmes et al., Structural mechanism of the recovery stroke in the myosin molecular motor, Proceedings of the National Academy of Sciences of the United States of America, vol.102, p.51, 2005.

S. Mesentean, S. Fischer, C. Jeremy, and . Smith, Analyzing large-scale structural change in proteins : Comparison of principal component projection and sammon mapping, Proteins : Structure, Function, and Bioinformatics, vol.64, p.51, 2006.

E. Laine, C. Goncalves, and J. C. Karst, Use of allostery to identify inhibitors of calmodulin-induced activation of Bacillus anthracis edema factor, Proceedings of the National Academy of Sciences, vol.107, p.51, 2010.
URL : https://hal.archives-ouvertes.fr/pasteur-01501815

P. Conti, L. Tamborini, and A. Pinto, Drug discovery targeting amino acid racemases, Chemical reviews, vol.111, p.51, 2011.

. Bibliographie,

S. Jo, T. Kim, G. Vidyashankara, W. Iyer, and . Im, CHARMM-GUI : a web-based graphical user interface for CHARMM, Journal of computational chemistry, vol.29, p.53, 2008.

M. Tung, . Fong, G. Mark, and . Mcnamee, Correlation between acetylcholine receptor function and structural properties of membranes, Biochemistry 25, vol.4, p.53, 1986.

. Mp-mccarthy, A. Marjorie, and . Moore, Effects of lipids and detergents on the conformation of the nicotinic acetylcholine receptor from Torpedo californica, In : Journal of Biological Chemistry, vol.267, p.53, 1992.

. Saffron-e-rankin, H. George, . Addona, A. Marek, B. Kloczewiak et al., The cholesterol dependence of activation and fast desensitization of the nicotinic acetylcholine receptor, Biophysical journal 73, vol.5, p.53, 1997.

A. A. Jb-corrie, E. A. Ogrel, . Mccardy, P. Michael, . Blanton et al., Lipid-protein interactions at the nicotinic acetylcholine receptor A functional coupling between nicotinic receptors and phosphatidic acid-containing lipid bilayers, Journal of Biological Chemistry, vol.277, p.53, 2002.

J. William-l-jorgensen, J. D. Chandrasekhar, . Madura, W. Roger, . Impey et al., Comparison of simple potential functions for simulating liquid water, The Journal of chemical physics, vol.79, issue.2, p.53, 1983.

M. Toulouse, . Fritsch, and . Westhof, Rapid Calculation of Any Dielectric Function for Molecular Dynamics Simulations of Biological Macromolecules, OA drug design & delivery, vol.9, p.54, 1992.

M. Jaiteh, A. Taly, and J. Hénin, Evolution of pentameric ligandgated ion channels : Pro-loop receptors, PloS one, vol.11, pp.151934-54, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01497980

B. Jeffery, R. M. Klauda, A. Venable, and . Freites, Update of the CHARMM all-atom additive force field for lipids : validation on six lipid types, The journal of physical chemistry B, vol.114, p.57, 2010.

V. Jeffery-b-klauda, T. Monje, W. Kim, and . Im, Improving the CHARMM force field for polyunsaturated fatty acid chains, The journal of physical chemistry B, vol.116, p.57, 2012.

K. Vanommeslaeghe, E. Hatcher, and C. Acharya, CHARMM general force field : A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields, Journal of computational chemistry, vol.31, p.57, 2010.

W. Yu, X. He, K. Vanommeslaeghe, D. Alexander, and . Mackerell, Extension of the CHARMM general force field to sulfonyl-containing compounds and its utility in biomolecular simulations, Journal of computational chemistry, vol.33, p.57, 2012.

D. Beglov and . Benoit-roux, Finite representation of an infinite bulk system : solvent boundary potential for computer simulations, The Journal of chemical physics, vol.100, p.57, 1994.

J. Ryckaert, G. Ciccotti, J. C. Herman, and . Berendsen, Numerical integration of the cartesian equations of motion of a system with constraints : molecular dynamics of n-alkanes, Journal of Computational Physics, vol.23, p.58, 1977.

. Antti-pekka-hynninen, F. Michael, and . Crowley, New faster CHARMM molecular dynamics engine, Journal of computational chemistry, vol.35, p.58, 2014.

J. Florian, M. Gisdon, M. Culka, and . Ullmann, PyCPR-a python-based implementation of the Conjugate Peak Refinement (CPR) algorithm for finding transition state structures, Journal of molecular modeling, vol.22, p.65, 2016.

D. Branduardi, D. José, and . Faraldo-gómez, String Method for Calculation of Minimum Free-Energy Paths in Cartesian Space in Freely Tumbling Systems, Journal of chemical theory and computation, vol.9, p.69, 2013.

C. Miller, Genetic manipulation of ion channels : a new approach to structure and mechanism, p.71

F. Revah, J. Bertrand, and . Galzi, Mutations in the channel domain alter desensitization of a neuronal nicotinic receptor, Nature, vol.353, p.70, 1991.

C. Labarca, W. Mark, H. Nowak, and . Zhang, Channel gating governed symmetrically by conserved leucine residues in the M2 domain of nicotinic receptors, Nature, vol.376, p.70, 1995.

N. Gregory, . Filatov, M. Michael, and . White, The role of conserved leucines in the M2 domain of the acetylcholine receptor in channel gating, Molecular Pharmacology, vol.48, p.70, 1995.

J. Changeux and A. Christopoulos, Allosteric modulation as a unifying mechanism for receptor function and regulation, In : Cell, vol.166, p.71, 2016.

N. Calimet, M. Simoes, and J. Changeux, A gating mechanism of pentameric ligand-gated ion channels, Proceedings of the National Academy of Sciences, p.71, 2013.
URL : https://hal.archives-ouvertes.fr/hal-01498070

B. August, K. Smit, N. Brejc, . Syed, K. Titia et al., Structure and function of AChBP, homologue of the ligand-binding domain of the nicotinic acetylcholine receptor, Annals of the New York Academy of Sciences, vol.998, issue.1, p.72, 2003.

S. E. Patrick-hn-celie, W. J. Van-rossum-fikkert, and . Van-dijk, Nicotine and carbamylcholine binding to nicotinic acetylcholine receptors as studied in AChBP crystal structures, Neuron, vol.41, p.72, 2004.

J. Changeux, J. Stuart, and . Edelstein, The brain as a chemical machine : nicotinic receptors and neuronal communication, Odile Jacob, p.72, 2012.

J. Pérez, J. Zanotti, and D. Durand, Evolution of the internal dynamics of two globular proteins from dry powder to solution, Biophysical journal, vol.77, p.81, 1999.

. Bibliographie,

R. Perozzo, G. Folkers, and L. Scapozza, Thermodynamics of proteinligand interactions : history, presence, and future aspects, Journal of Receptors and Signal Transduction, vol.24, issue.1-2, p.86, 2004.

J. Liang, C. Woodward, and H. Edelsbrunner, Anatomy of protein pockets and cavities : measurement of binding site geometry and implications for ligand design, Protein science, vol.7, p.86, 1998.

A. Mark, J. M. Williams, . Goodfellow, M. Janet, and . Thornton, Buried waters and internal cavities in monomeric proteins, Protein Science, vol.3, p.86, 1994.

S. Kortagere, D. Matthew, S. Krasowski, and . Ekins, The importance of discerning shape in molecular pharmacology, Trends in pharmacological sciences, vol.30, p.86, 2009.

J. Alvarez and B. Shoichet, Virtual screening in drug discovery, p.86, 2005.

A. Jennings, Chemical Informatics : Using Molecular Shape Descriptors in Structure-Based Drug Design, Structure-Based Drug Discovery, p.86, 2012.

K. Nataraj-s-pagadala, J. Syed, and . Tuszynski, Software for molecular docking : a review, Biophysical reviews, vol.9, issue.2, p.86, 2017.

C. Amy and . Anderson, The process of structure-based drug design, Chemistry & biology, vol.10, p.86, 2003.

M. Congreve, W. Christopher, . Murray, L. Tom, and . Blundell, Keynote review : Structural biology and drug discovery, Drug discovery today, vol.10, p.86, 2005.

J. Ko, L. F. Murga, Y. Wei, and M. J. Ondrechen, Prediction of active sites for protein structures from computed chemical properties, Bioinformatics 21.suppl_1, p.86, 2005.

S. Sankararaman, F. Sha, F. Jack, M. Kirsch, . Et-kimmen et al., Active site prediction using evolutionary and structural information, Bioinformatics, vol.26, p.86, 2010.

T. Craig, G. J. Porter, . Bartlett, M. Janet, and . Thornton, The Catalytic Site Atlas : a resource of catalytic sites and residues identified in enzymes using structural data, Nucleic acids research, vol.32, p.86, 2004.

A. Christopoulos, Allosteric binding sites on cell-surface receptors : novel targets for drug discovery, Nature reviews Drug discovery, vol.1, issue.3, p.86, 2002.

J. Conn, A. Christopoulos, W. Craig, and . Lindsley, Allosteric modulators of GPCRs : a novel approach for the treatment of CNS disorders, Nature reviews Drug discovery, vol.8, issue.1, p.86, 2009.

T. Lauren, K. May, . Leach, M. Patrick, A. Sexton et al., Allosteric modulation of G protein-coupled receptors, Annu. Rev. Pharmacol. Toxicol, vol.47, p.86, 2007.

J. Yang, S. W. Seo, S. Jang, and G. Kim, Rational engineering of enzyme allosteric regulation through sequence evolution analysis, PLoS computational biology, vol.8, issue.7, p.86, 2012.

A. Christopoulos, . May, . Va-avlani, and . Sexton, G-protein-coupled receptor allosterism : the promise and the problem (s). 2004 (cf, p.86

T. Kenakin, J. Laurence, and . Miller, Seven transmembrane receptors as shapeshifting proteins : the impact of allosteric modulation and functional selectivity on new drug discovery, Pharmacological reviews, p.86, 2010.

Z. Fang, C. Grütter, and D. Rauh, Strategies for the selective regulation of kinases with allosteric modulators : exploiting exclusive structural features, ACS chemical biology, vol.8, issue.1, p.86, 2012.

S. Lu, W. Huang, and J. Zhang, Recent computational advances in the identification of allosteric sites in proteins, Drug discovery today, vol.19, p.86, 2014.

W. Huang, R. Nussinov, and J. Zhang, Computational Tools for Allosteric Drug Discovery : Site Identification and Focus Library Design, Computational Protein Design, p.86, 2017.

G. Joe, . Greener, J. E. Michael, and . Sternberg, Structure-based prediction of protein allostery, Current opinion in structural biology, vol.50, p.86, 2018.

J. Stephen, S. Benkovic, and . Hammes-schiffer, A perspective on enzyme catalysis, Science, vol.301, pp.1196-1202, 2003.

D. Antoniou, D. Steven, and . Schwartz, Internal enzyme motions as a source of catalytic activity : rate-promoting vibrations and hydrogen tunneling, The Journal of Physical Chemistry B, vol.105, pp.5553-5558, 2001.

S. Vishal-c-nashine, . Hammes-schiffer, J. Stephen, and . Benkovic, Coupled motions in enzyme catalysis, Current opinion in chemical biology, vol.14, pp.644-651, 2010.

R. F. Tilton, I. D. Kuntz, and G. A. Petsko, Cavities in proteins : structure of a metmyoglobin xenon complex solved to 1.9, Biochemistry 23.13 (juin 1984), vol.97, p.87

M. Brunori, H. Quentin, and . Gibson, Cavities and packing defects in the structural dynamics of myoglobin, EMBO reports, vol.2, pp.674-679, 2001.

D. Jory-z-ruscio, M. Kumar, and . Shukla, Atomic level computational identification of ligand migration pathways between solvent and binding site in myoglobin, Proceedings of the National Academy of Sciences 105, vol.27, pp.9204-9209, 2008.

C. Bossa, A. Amadei, and I. Daidone, Molecular dynamics simulation of sperm whale myoglobin : effects of mutations and trapped CO on the structure and dynamics of cavities, Biophysical journal, vol.89, pp.465-474, 2005.

A. Tomita, T. Sato, and K. Ichiyanagi, Visualizing breathing motion of internal cavities in concert with ligand migration in myoglobin, Proceedings of the National Academy of Sciences, vol.106, pp.2612-2616, 2009.

. Bibliographie,

M. A. Scorciapino, A. Robertazzi, M. Casu, P. Ruggerone, and M. Ceccarelli, Breathing motions of a respiratory protein revealed by molecular dynamics simulations, Journal of the American Chemical Society, vol.131, pp.11825-11832, 2009.

M. Gabba, S. Abbruzzetti, and F. Spyrakis, CO rebinding kinetics and molecular dynamics simulations highlight dynamic regulation of internal cavities in human cytoglobin, PLoS One, vol.8, issue.1, p.49770, 2013.

A. Mee-kian-poh, S. Yip, and . Zhang, A small molecule fusion inhibitor of dengue virus, Antiviral Res, vol.84, issue.3, p.87

W. Tang and Q. Guo, The adenylyl cyclase activity of anthrax edema factor, Molecular aspects of medicine, vol.30, pp.423-430, 2009.

Z. Huang, L. Zhu, and Y. Cao, ASD : a comprehensive database of allosteric proteins and modulators, Nucleic acids research 39.suppl_1 (2010), vol.87, pp.663-669

S. Eyrisch and V. Helms, Transient pockets on protein surfaces involved in protein-protein interaction, Journal of medicinal chemistry, vol.50, pp.3457-3464, 2007.

M. Nayal and B. Honig, On the nature of cavities on protein surfaces : application to the identification of drug-binding sites, Proteins : Structure, Function, and Bioinformatics, vol.63, pp.892-906, 2006.

S. Pérot, O. Sperandio, M. A. Miteva, A. Camproux, O. Bruno et al., Druggable pockets and binding site centric chemical space : a paradigm shift in drug discovery, Drug discovery today, vol.15, pp.656-667, 2010.

H. Claußen, C. Buning, M. Rarey, and T. Lengauer, FlexE : efficient molecular docking considering protein structure variations, Journal of molecular biology, vol.308, pp.377-395, 2001.

A. M. Ferrari, Q. Binqing, L. Wei, . Costantino, K. Brian et al., Soft docking and multiple receptor conformations in virtual screening, Journal of medicinal chemistry, vol.47, pp.5076-5084, 2004.

S. Cosconati, L. Marinelli, and F. Leva, Protein flexibility in virtual screening : the BACE-1 case study, Journal of chemical information and modeling, vol.52, pp.2697-2704, 2012.

M. Krone, B. Kozlíková, and N. Lindow, Visual Analysis of Biomolecular Cavities : State of the Art, Comput. Graph. Forum, vol.35, issue.3, p.87, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01400464

T. Simões, D. Lopes, and S. Dias, Geometric detection algorithms for cavities on protein surfaces in molecular graphics : a survey, Computer Graphics Forum. T. 36. 8. Wiley Online Library, vol.87, pp.643-683, 2017.

B. Ma, M. Shatsky, J. Haim, R. Wolfson, and . Nussinov, Multiple diverse ligands binding at a single protein site : A matter of pre-existing populations, Protein science, vol.11, issue.2, pp.184-197, 2002.

C. Globisch, K. Ilza, M. Pajeva, and . Wiese, Identification of Putative Binding Sites of P-glycoprotein Based on its Homology Model, vol.3, pp.280-295, 2008.

L. Carlos-a-fuzo and . Degrève, New pockets in dengue virus 2 surface identified by molecular dynamics simulation, J. Mol. Model, vol.19, issue.3, p.87, 2013.

R. Diskin, D. Engelberg, and O. Livnah, A novel lipid binding site formed by the MAP kinase insert in p38?, Journal of molecular biology, vol.375, pp.70-79, 2008.

N. Lindow, D. Baum, A. Bondar, and H. Hege, Exploring cavity dynamics in biomolecular systems, BMC bioinformatics, vol.14, p.88, 2013.

N. Desdouits, Concepts et méthodes d'analyse numérique de la dynamique des cavités au sein des protéines et applications à l'élaboration de stratégies novatrices d'inhibition, vol.167, p.99, 2015.

G. Sandra-w-cowan-jacob, A. Fendrich, and . Floersheimer, Structural biology contributions to the discovery of drugs to treat chronic myelogenous leukaemia, Acta Crystallographica Section D : Biological Crystallography, vol.63, p.97, 2007.

Y. Modis, S. Ogata, D. Clements, C. Stephen, and . Harrison, A ligandbinding pocket in the dengue virus envelope glycoprotein, In : Proc. Natl. Acad. Sci. U. S. A. 100, vol.12, p.97, 2003.

S. Chester-l-drum, J. Yan, and . Bard, Structural basis for the activation of anthrax adenylyl cyclase exotoxin by calmodulin, Nature, vol.415, p.97, 2002.

B. Lee and F. M. Richards, The interpretation of protein structures : Estimation of static accessibility, Journal of Molecular Biology, vol.55, p.97, 1971.

L. Michael and . Connolly, Solvent-accessible surfaces of proteins and nucleic acids, Science 221, vol.4612, p.97, 1983.

. A_-bondi, der Waals volumes and radii, vol.68, p.97, 1964.

G. Linda, . Shapiro, . Linda-;-stockman, and C. George, Computer Vision, p.98, 0200.

E. Jones, T. Oliphant, and P. Peterson, SciPy : Open source scientific tools for Python

F. Pedregosa, G. Varoquaux, and A. Gramfort, Scikit-learn : Machine Learning in Python, Journal of Machine Learning Research, vol.12, p.99, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00650905

. Bibliographie,

B. Larsen and C. Aone, Fast and effective text mining using linear-time document clustering, Proc. fifth ACM SIGKDD Int. Conf. Knowl. Discov. data Min. -KDD '99, p.102, 1999.

. R-tyrrell-rockafellar, J. Roger, and . Wets, , p.103, 2009.

S. Hubbard and . Argos, Cavities and packing at protein interfaces, In : Protein science : a publication of the Protein Society, vol.3, p.105

J. Simon, K. Hubbard, P. Gross, and . Argos, Intramolecular cavities in globular proteins, Protein Engineering, p.105

S. Sonavane and P. Chakrabarti, Cavities and Atomic Packing in Protein Structures and Interfaces, PLoS Computational Biology, vol.4, p.105, 2008.

C. Charu, A. Aggarwal, . Hinneburg, A. Daniel, and . Keim, On the Surprising Behavior of Distance Metrics in High Dimensional Space, p.108, 2001.

T. Schindler, Structural Mechanism for STI-571 Inhibition of Abelson Tyrosine Kinase". en, Science 289.5486 (sept. 2000), p.109

J. Zhang, J. Francisco, W. Adrián, and . Jahnke, Targeting Bcr-Abl by combining allosteric with ATP-binding-site inhibitors, Nature, vol.463, p.109, 2010.

R. Yennamalli, N. Subbarao, and T. Kampmann, Identification of novel target sites and an inhibitor of the dengue virus E protein, J. Comput. Aided. Mol. Des, vol.23, issue.6, p.109, 2009.

A. L. Bodnar, L. A. Cortes-burgos, and K. K. Cook, Discovery and structureactivity relationship of quinuclidine benzamides as agonists of ?7 nicotinic acetylcholine receptors, Journal of medicinal chemistry, vol.48, p.132, 2005.

M. Hajos, . Hurst, and . Hoffmann, The selective ?7 nicotinic acetylcholine receptor agonist PNU-282987 [N-[(3R)-1-azabicyclo [2.2. 2] oct-3-yl]-4-chlorobenzamide hydrochloride] enhances GABAergic synaptic activity in brain slices and restores auditory gating deficits in anesthetized rats, Journal of Pharmacology and Experimental Therapeutics, vol.312, p.132, 2005.

. Ca-briggs, . Schrimpf, and . Anderson, ?7 nicotinic acetylcholine receptor agonist properties of tilorone and related tricyclic analogues, British journal of pharmacology, vol.153, p.132, 2008.

. William-r-kem, The brain ?7 nicotinic receptor may be an important therapeutic target for the treatment of Alzheimer's disease : studies with DMXBA (GTS-21), Behavioural brain research, vol.113, p.132, 2000.

J. M. Ward, . Cockcroft, . Lunt, . Fs-smillie, and . Wonnacott, Methyllycaconitine : a selective probe for neuronal ?-bungarotoxin binding sites, FEBS letters, vol.270, p.132, 1990.

J. A. Michael-j-marks, E. Stitzel, J. Romm, A. Wehner, and . Collins, Nicotinic binding sites in rat and mouse brain : comparison of acetylcholine, nicotine, and alpha-bungarotoxin, In : Molecular pharmacology, vol.30, p.132, 1986.

A. Hugo-r-arias, . Rosenberg, M. Katarzyna, and . Targowska-duda, Tricyclic antidepressants and mecamylamine bind to different sites in the human ?4?2 nicotinic receptor ion channel, The international journal of biochemistry & cell biology, vol.42, p.132, 2010.

K. Jaskiran, P. Gill-thind, . Dhankher, M. Jarryl, . Oyley et al., Structurally similar allosteric modulators of ?7 nicotinic acetylcholine receptors exhibit five distinct pharmacological effects, Journal of Biological Chemistry, vol.159, p.132, 2014.

A. Chatzidaki, S. Neil, and . Millar, Allosteric modulation of nicotinic acetylcholine receptors, Biochemical pharmacology 97, vol.4, p.132, 2015.

E. Pihan, L. Colliandre, J. Guichou, and D. Douguet, e-Drug3D : 3D structure collections dedicated to drug repurposing and fragmentbased drug design, Bioinformatics, vol.28, p.133, 2012.
URL : https://hal.archives-ouvertes.fr/hal-02115767

K. Dustin, C. Williams, . Peng, R. Matthew, . Kimbrell et al., Intrinsically low open probability of ?7 nicotinic acetylcholine receptors can be overcome by positive allosteric modulation and serum factors leading to the generation of excitotoxic currents at physiological temperatures, Molecular pharmacology, vol.82, p.133, 2012.

M. Guerra-Álvarez, A. J. Moreno-ortega, and E. Navarro, Positive allosteric modulation of alpha-7 nicotinic receptors promotes cell death by inducing Ca2+ release from the endoplasmic reticulum, Journal of neurochemistry, vol.133, p.133, 2015.

M. Rarey, B. Kramer, T. Lengauer, and G. Klebe, A fast flexible docking method using an incremental construction algorithm, Journal of molecular biology, vol.261, p.133, 1996.

A. Dennis and . Dougherty, Cys-loop neuroreceptors : structure to the rescue ?, In : Chemical reviews, vol.108, p.135, 2008.

J. Galzi, D. Bertrand, and A. Devillers-thiéry, Functional significance of aromatic amino acids from three peptide loops of the ?7 neuronal nicotinic receptor site investigated by site-directed mutagenesis, FEBS letters, vol.294, p.135, 1991.
URL : https://hal.archives-ouvertes.fr/hal-02193481

W. Zhong, J. P. Gallivan, and Y. Zhang, From ab initio quantum mechanics to molecular neurobiology : a cation-? binding site in the nicotinic receptor, Proceedings of the National Academy of Sciences 95, vol.21, p.135, 1998.

P. Corringer, N. L. Novère, and J. Changeux, Nicotinic receptors at the amino acid level, Annual review of pharmacology and toxicology, vol.40, p.135, 2000.
URL : https://hal.archives-ouvertes.fr/pasteur-01719004

C. Jennifer, . Ma, A. Dennis, and . Dougherty, The cation-? interaction, Chemical reviews 97, vol.5, p.135, 1997.

. Bibliographie,

S. Mecozzi, P. Anthony, . West, A. Dennis, and . Dougherty, Cation-? interactions in simple aromatics : electrostatics provide a predictive tool, Journal of the American Chemical Society, vol.118, p.135, 1996.

A. Dennis and . Dougherty, The cation-? interaction, Accounts of chemical research, vol.46, p.135, 2012.

J. Liu and R. Wang, Classification of current scoring functions, Journal of chemical information and modeling, vol.55, p.135, 2015.

R. Sayle, 1st-class SMARTS patterns, EuroMUG 97, p.136, 1997.

S. Mark-m-levandoski and . Koganti, Allosteric Modulation of Neuronal Nicotinic Acetylcholine Receptors, Allosterism in Drug Discovery, p.137, 2016.

R. Dey and L. Chen, In search of allosteric modulators of ?7-nAChR by solvent density guided virtual screening, Journal of Biomolecular Structure and Dynamics, vol.28, p.142, 2011.

D. Bertrand, S. Bertrand, and S. Cassar, Positive allosteric modulation of the ?7 nicotinic acetylcholine receptor : ligand interactions with distinct binding sites and evidence for a prominent role of the M2-M3 segment, Molecular pharmacology, vol.74, p.142, 2008.

X. Hu, M. David, and . Lovinger, The L293 residue in transmembrane domain 2 of the 5-HT3A receptor is a molecular determinant of allosteric modulation by 5-hydroxyindole, Neuropharmacology, vol.54, p.142, 2008.

A. Clark, J. H. Briggs, P. Grønlien, and . Curzon, Role of channel activation in cognitive enhancement mediated by ?7 nicotinic acetylcholine receptors, British journal of pharmacology, vol.158, p.142, 2009.

T. Collins, T. Gareth, . Young, S. Neil, and . Millar, Competitive binding at a nicotinic receptor transmembrane site of two ?7-selective positive allosteric modulators with differing effects on agonist-evoked desensitization, Neuropharmacology, vol.61, p.159, 2011.

H. Christof and . Schwab, Conformations and 3D pharmacophore searching, Drug Discovery Today : Technologies, vol.7, p.142, 2010.

. Marvin--chemaxon, Marvin was used for drawing, displaying and characterizing chemical structures, substructures and reactions (cf, -Software Solutions and Services for Chemistry, p.142

M. Noel, M. Boyle, . Banck, A. Craig, and . James, Open Babel : An open chemical toolbox, Journal of cheminformatics, vol.3, p.142, 2011.

J. Kiener, Molecule database framework : a framework for creating database applications with chemical structure search capability, Journal of cheminformatics, vol.5, p.142, 2013.

. Eric-f-pettersen, D. Thomas, . Goddard, C. Conrad, and . Huang, UCSF Chimera-a visualization system for exploratory research and analysis, In : Journal of computational chemistry, vol.25, p.142, 2004.

M. Garrett, R. Morris, W. Huey, and . Lindstrom, AutoDock4 and AutoDock-Tools4 : Automated docking with selective receptor flexibility, Journal of computational chemistry, vol.30, pp.142-144, 2009.

O. Trott, J. Arthur, and . Olson, AutoDock Vina : improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading, Journal of computational chemistry, vol.31, p.143, 2010.

J. William, T. E. Allen, S. Balius, and . Mukherjee, DOCK 6 : impact of new features and current docking performance, Journal of computational chemistry, vol.36, p.143, 2015.

T. Lang, S. Scott-r-brozell, and . Mukherjee, DOCK 6 : Combining techniques to model RNA-small molecule complexes, Rna, p.143, 2009.

N. Schneider, G. Lange, S. Hindle, R. Klein, and M. Rarey, A consistent description of HYdrogen bond and DEhydration energies in proteinligand complexes : methods behind the HYDE scoring function, Journal of computer-aided molecular design, vol.27, p.144, 2013.

M. Wójcikowski, J. Pedro, P. Ballester, and . Siedlecki, Performance of machinelearning scoring functions in structure-based virtual screening, Scientific Reports, vol.7, p.144, 2017.

, RF-Score-VS -Random forest based protein-ligand scoring function for Virtual Screening

Y. Cao and L. Li, Improved protein-ligand binding affinity prediction by using a curvature-dependent surface-area model, Bioinformatics, vol.30, p.144, 2014.

. David-ryan-koes, P. Matthew, . Baumgartner, J. Carlos, and . Camacho, Lessons learned in empirical scoring with smina from the CSAR 2011 benchmarking exercise, Journal of chemical information and modeling, vol.53, p.144, 2013.

R. Quiroga, A. Marcos, and . Villarreal, Vinardo : A scoring function based on autodock vina improves scoring, docking, and virtual screening, PloS one, vol.11, pp.155183-144, 2016.

, Scoring and Minimization with AutoDock Vina

G. Chessari, A. Christopher, . Hunter, M. R. Caroline, and . Low, An evaluation of force-field treatments of aromatic interactions, Chemistry-A European Journal, vol.8, p.144, 2002.

T. Pymol, The PyMOL molecular graphics system, p.145, 2010.

V. Bondarenko, D. David, T. S. Mowrey, and . Tillman, NMR structures of the human ?7 nAChR transmembrane domain and associated anesthetic binding sites, Biochimica Et Biophysica Acta (BBA)-Biomembranes, vol.1838, p.156, 2014.

. Jb-corrie, M. Steven, and . Sine, Stoichiometry for drug potentiation of a pentameric ion channel, Proceedings of the National Academy of Sciences, p.156, 2013.

. Bibliographie,

T. Collins, S. Neil, and . Millar, Nicotinic acetylcholine receptor transmembrane mutations convert ivermectin from a positive to a negative allosteric modulator, Molecular pharmacology, vol.160, p.156, 2010.

J. Galzi, S. Bertrand, P. Corringer, J. Changeux, and D. Bertrand, Identification of calcium binding sites that regulate potentiation of a neuronal nicotinic acetylcholine receptor, The EMBO Journal, vol.15, p.158, 1996.
URL : https://hal.archives-ouvertes.fr/pasteur-01715606

M. Nys, E. Wijckmans, and A. Farinha, Allosteric binding site in a Cysloop receptor ligand-binding domain unveiled in the crystal structure of ELIC in complex with chlorpromazine, Proceedings of the National Academy of Sciences, vol.113, p.158, 2016.

M. Ryoko, B. Krause, S. Buisson, and . Bertrand, Ivermectin : a positive allosteric effector of the ?7 neuronal nicotinic acetylcholine receptor, Molecular pharmacology, vol.53, p.159, 1998.

F. Deba, I. Hamed, A. Ali, and . Tairu, LY2087101 and dFBr share transmembrane binding sites in the (?4) 3 (?2) 2 Nicotinic Acetylcholine Receptor, Scientific reports, vol.8, p.160, 2018.

, CDP6 Components Report for SGA1 M13-M24, PDF format, p.168

A. Meijster, B. Jos, . Roerdink, H. Wim, and . Hesselink, A general algorithm for computing distance transforms in linear time, Mathematical Morphology and its applications to image and signal processing, pp.331-340, 0200.

M. Stephen and . Omohundro, Five balltree construction algorithms, 0200.

L. Dagum and R. Menon, OpenMP : an industry standard API for shared-memory programming, Computational Science & Engineering, IEEE, vol.5, pp.46-55, 0200.

, OpenMP Application Program Interface Version 3.0, 2008.

S. Michiel-jl-de-hoon, J. Imoto, S. Nolan, and . Miyano, Open source clustering software, Bioinformatics, vol.20, pp.1453-1454, 0200.