S. J. Wodak and J. Janin, Structural basis of macromolecular recognition, Protein Modules and Protein?Protein Interaction, pp.9-73, 2002.
DOI : 10.1016/S0065-3233(02)61001-0

K. D. Corbett and T. Alber, The many faces of Ras: recognition of small GTP-binding proteins, Trends in Biochemical Sciences, vol.26, issue.12, pp.710-716, 2001.
DOI : 10.1016/S0968-0004(01)01974-0

R. L. Desjarlais, R. P. Sheridan, G. L. Seibel, S. J. Dixon, I. D. Kuntz et al., Using shape complementarity as an initial screen in designing ligands for a receptor binding site of known three-dimensional structure, Journal of Medicinal Chemistry, vol.31, issue.4, pp.722-729, 1988.
DOI : 10.1021/jm00399a006

R. Chen and Z. Weng, A novel shape complementarity scoring function for protein-protein docking, Proteins: Structure, Function, and Genetics, vol.51, issue.3, pp.397-408, 2003.
DOI : 10.1002/prot.10334

C. M. Venkatachalam, X. Jiang, T. Oldfield, and M. Waldman, LigandFit: a novel method for the shape-directed rapid docking of ligands to protein active sites, Journal of Molecular Graphics and Modelling, vol.21, issue.4, pp.289-307, 2003.
DOI : 10.1016/S1093-3263(02)00164-X

A. E. Eriksson, W. A. Baase, X. Zhang, D. W. Heinz, M. Blaber et al., Response of a protein structure to cavity-creating mutations and its relation to the hydrophobic effect, Science, vol.255, issue.5041, pp.178-183, 1992.
DOI : 10.1126/science.1553543

R. Elber and M. Karplus, Enhanced sampling in molecular dynamics: use of the time-dependent Hartree approximation for a simulation of carbon monoxide diffusion through myoglobin, Journal of the American Chemical Society, vol.112, issue.25, pp.9161-9175, 1990.
DOI : 10.1021/ja00181a020

R. Elber, Ligand diffusion in globins: simulations versus experiment, Current Opinion in Structural Biology, vol.20, issue.2, pp.162-167, 2010.
DOI : 10.1016/j.sbi.2010.01.002

R. C. Wade, P. J. Winn, and I. Schlichting, A survey of active site access channels in cytochromes P450, Journal of Inorganic Biochemistry, vol.98, issue.7, pp.1175-1182, 2004.
DOI : 10.1016/j.jinorgbio.2004.02.007

Y. Miao and J. Baudry, Active-Site Hydration and Water Diffusion in Cytochrome P450cam: A??Highly Dynamic Process, Biophysical Journal, vol.101, issue.6, pp.1493-1503, 2011.
DOI : 10.1016/j.bpj.2011.08.020

A. G. Watts, I. Damager, M. L. Amaya, A. Buschiazzo, P. Alzari et al., Trypanosoma cruzi trans-sialidase operates through a covalent sialylenzyme intermediate: tyrosine is the catalytic nucleophile, J. Am. Chem. Soc, issue.25, pp.125-7532, 2003.

S. Liu, J. S. Chang, J. T. Herberg, M. Horng, P. K. Tomich et al., Allosteric inhibition of Staphylococcus aureus D-alanine:D-alanine ligase revealed by crystallographic studies, Proceedings of the National Academy of Sciences, vol.103, issue.41, pp.15178-15183, 2006.
DOI : 10.1073/pnas.0604905103

R. D. Vale and R. A. Milligan, The Way Things Move: Looking Under the Hood of Molecular Motor Proteins, Science, vol.288, issue.5463, pp.88-95, 2000.
DOI : 10.1126/science.288.5463.88

J. Simon, P. Hubbard, and . Argos, Cavities and packing at protein interfaces, Protein Sci, vol.3, issue.12, pp.2194-2206, 1994.

S. Sonavane and P. Chakrabarti, Cavities and Atomic Packing in Protein Structures and Interfaces, PLoS Computational Biology, vol.22, issue.9, pp.1000188-1000197, 2008.
DOI : 10.1371/journal.pcbi.1000188.s010

S. Eyrisch and V. Helms, What induces pocket openings on protein surface patches involved in protein???protein interactions?, Journal of Computer-Aided Molecular Design, vol.350, issue.2, pp.73-86, 2009.
DOI : 10.1007/s10822-008-9239-y

C. Bossa, A. Amadei, I. Daidone, M. Anselmi, B. Vallone et al., Molecular Dynamics Simulation of Sperm Whale Myoglobin: Effects of Mutations and Trapped CO on the Structure and Dynamics of Cavities, Biophysical Journal, vol.89, issue.1, pp.465-474, 2005.
DOI : 10.1529/biophysj.104.055020

J. Z. Ruscio, D. Kumar, M. Shukla, M. G. Prisant, T. M. Murali et al., Atomic level computational identification of ligand migration pathways between solvent and binding site in myoglobin, Proceedings of the National Academy of Sciences, vol.105, issue.27, pp.9204-9209, 2008.
DOI : 10.1073/pnas.0710825105

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, issue.33, pp.11825-11832, 2009.
DOI : 10.1021/ja9028473

M. Gabba, S. Abbruzzetti, F. Spyrakis, F. Forti, S. Bruno et al., Moens, S. Dewilde, CO rebinding kinetics and molecular dynamics simulations highlight dynamic regulation of internal cavities in human cytoglobin, PLOS ONE, vol.8, issue.49770, p.1, 2013.

S. Eyrisch and V. Helms, Transient Pockets on Protein Surfaces Involved in Protein???Protein Interaction, Journal of Medicinal Chemistry, vol.50, issue.15, pp.3457-3464, 2007.
DOI : 10.1021/jm070095g

P. Schmidtke, A. Bidon-chanal, F. J. Luque, and X. Barril, MDpocket: open-source cavity detection and characterization on molecular dynamics trajectories, Bioinformatics, vol.27, issue.23, pp.3276-3285, 2011.
DOI : 10.1093/bioinformatics/btr550

URL : http://bioinformatics.oxfordjournals.org/cgi/content/short/27/23/3276

M. Krone, M. Falk, S. Rehm, J. Pleiss, and T. Ertl, Interactive Exploration of Protein Cavities, Computer Graphics Forum, vol.1, issue.1, pp.673-682, 2011.
DOI : 10.1111/j.1467-8659.2011.01916.x

A. Metz, C. Pfleger, H. Kopitz, S. Pfeiffer-marek, K. Baringhaus et al., Hot Spots and Transient Pockets: Predicting the Determinants of Small-Molecule Binding to a Protein???Protein Interface, Journal of Chemical Information and Modeling, vol.52, issue.1, pp.120-133, 2012.
DOI : 10.1021/ci200322s

P. Ashford, D. Moss, A. Alex, S. Yeap, A. Povia et al., Visualisation of variable binding pockets on protein surfaces by probabilistic analysis of related structure sets, BMC Bioinformatics, vol.13, issue.1, 2012.
DOI : 10.1186/1471-2105-13-39

D. B. Kokh, S. Richter, S. Henrich, P. Czodrowski, F. Rippmann et al., roteins, Journal of Chemical Information and Modeling, vol.53, issue.5, pp.1235-1252, 2013.
DOI : 10.1021/ci4000294

B. Lee and F. M. Richards, The interpretation of protein structures: Estimation of static accessibility, Journal of Molecular Biology, vol.55, issue.3, pp.379-400, 1971.
DOI : 10.1016/0022-2836(71)90324-X

M. L. Connolly, Solvent-accessible surfaces of proteins and nucleic acids, Science, vol.221, issue.4612, pp.709-713, 1983.
DOI : 10.1126/science.6879170

J. Liang, C. Woodward, C. Woodward, H. Edelsbrunner, and H. Edelsbrunner, Anatomy of protein pockets and cavities: Measurement of binding site geometry and implications for ligand design, Protein Science, vol.245, issue.9, pp.1884-1897, 1998.
DOI : 10.1002/pro.5560070905

S. J. Lee, M. S. Mccormick, S. J. Lippard, and U. Cho, Control of substrate access to the active site in methane monooxygenase, Nature, vol.66, issue.7437, pp.380-384, 2013.
DOI : 10.1038/nature11880

B. W. Matthews, Structural and genetic analysis of the folding and function of t4 lysozyme, FASEB J, vol.10, issue.1, pp.35-41, 1996.

S. J. Hubbard and P. Argos, A Functional Role for Protein Cavities in Domain:Domain Motions, Journal of Molecular Biology, vol.261, issue.2, pp.289-300, 1996.
DOI : 10.1006/jmbi.1996.0460

Y. Modis, S. Ogata, D. Clements, and S. C. Harrison, Structure of the dengue virus envelope protein after membrane fusion, Nature, vol.427, issue.6972, pp.313-319, 2004.
DOI : 10.1038/nature02165

E. Laine, C. Goncalves, J. C. Karst, A. Lesnard, S. Rault et al., Use of allostery to identify inhibitors of calmodulin-induced activation of Bacillus anthracis edema factor, Proceedings of the National Academy of Sciences, vol.107, issue.25, pp.11277-11282, 2010.
DOI : 10.1073/pnas.0914611107

I. D. Kuntz, J. M. Blaney, S. J. Oatley, R. Langridge, and T. E. Ferrin, A geometric approach to macromolecule-ligand interactions, Journal of Molecular Biology, vol.161, issue.2, pp.269-288, 1982.
DOI : 10.1016/0022-2836(82)90153-X

S. Pérot, S. Olivier, M. A. Miteva, A. Camproux, and B. O. Villoutreix, Druggable pockets and binding site centric chemical space: a paradigm shift in drug discovery, Drug Discovery Today, vol.15, issue.15-16, pp.15-16, 2010.
DOI : 10.1016/j.drudis.2010.05.015

C. B. -rao, J. Subramanian, and S. D. Sharma, Managing protein flexibility in docking and its applications, Drug Discov. Today, vol.14, pp.7-8, 2009.

J. D. Durrant and J. A. Mccammon, Computer-aided drug-discovery techniques that account for receptor flexibility, Current Opinion in Pharmacology, vol.10, issue.6, pp.770-774, 2010.
DOI : 10.1016/j.coph.2010.09.001

R. H. Luecke, P. Lathrop, R. E. Kaiser, and . Amaro, Computational identification of a transiently open l1/s3 pocket for reactivation of mutant p53, Nat. Commun, vol.4, 1407.

I. M. Withers, M. P. Mazanetz, H. Wang, P. M. Fischer, and C. A. Laughton, Active Site Pressurization: A New Tool for Structure-Guided Drug Design and Other Studies of Protein Flexibility, Journal of Chemical Information and Modeling, vol.48, issue.7, pp.48-1448, 2008.
DOI : 10.1021/ci7004725

R. Abagyan and I. Kufareva, The Flexible Pocketome Engine for Structural Chemogenomics, Chemogenomics, pp.249-279, 2009.
DOI : 10.1007/978-1-60761-274-2_11

G. Bottegoni, I. Kufareva, M. Totrov, and R. Abagyan, A new method for ligand docking to flexible receptors by dual alanine scanning and refinement (SCARE), Journal of Computer-Aided Molecular Design, vol.50, issue.5, pp.311-325, 2008.
DOI : 10.1007/s10822-008-9188-5

T. Kawabata, Detection of multiscale pockets on protein surfaces using mathematical morphology, Proteins: Structure, Function, and Bioinformatics, vol.28, issue.5, pp.1195-1211, 2010.
DOI : 10.1002/prot.22639

R. F. Tilton, I. D. Kuntz, and G. A. Petsko, Cavities in proteins: structure of a metmyoglobin xenon complex solved to 1.9 .ANG., Biochemistry, vol.23, issue.13, pp.2849-2857, 1984.
DOI : 10.1021/bi00308a002

L. Maragliano, G. Cottone, G. Ciccotti, and E. , Mapping the Network of Pathways of CO Diffusion in Myoglobin, Journal of the American Chemical Society, vol.132, issue.3, pp.1010-1017, 2010.
DOI : 10.1021/ja905671x

A. Amadei, M. A. Ceruso, and A. D. Nola, On the convergence of the conformational coordinates basis set obtained by the essential dynamics analysis of proteins' molecular dynamics simulations, Proteins: Structure, Function, and Genetics, vol.35, issue.4, pp.419-424, 1999.
DOI : 10.1002/(SICI)1097-0134(19990901)36:4<419::AID-PROT5>3.0.CO;2-U

J. C. Phillips, R. Braun, W. Wang, J. Gumbart, E. Tajkhorshid et al., Scalable molecular dynamics with NAMD, Journal of Computational Chemistry, vol.84, issue.16, pp.26-1781, 2005.
DOI : 10.1002/jcc.20289

H. L. Venable, X. Woodcock, W. Wu, D. M. Yang, M. York et al., CHARMM: the biomolecular simulation program, J. Comput. Chem, vol.30, issue.10, pp.1545-1614, 2009.

M. Ester, H. Kriegel, J. Sander, and X. Xu, A density-based algorithm for discovering clusters in large spatial databases with noise KDD, pp.226-231, 1996.

L. Benkaidali, F. André, B. Maouche, P. Siregar, M. Benyettou et al., Computing cavities, channels, pores and pockets in proteins from non-spherical ligands models, Bioinformatics, vol.30, issue.6, pp.792-800, 2014.
DOI : 10.1093/bioinformatics/btt644

J. Abramson, I. Smirnova, V. Kasho, G. Verner, H. R. Kaback et al., Structure and Mechanism of the Lactose Permease of Escherichia coli, Science, vol.301, issue.5633, pp.610-615, 2003.
DOI : 10.1126/science.1088196

I. Smirnova, V. Kasho, J. Sugihara, and H. R. Kaback, Opening the periplasmic cavity in lactose permease is the limiting step for sugar binding, Proceedings of the National Academy of Sciences, vol.108, issue.37, pp.15147-15151, 2011.
DOI : 10.1073/pnas.1112157108

V. Chaptal, S. Kwon, M. R. Sawaya, L. Guan, H. Ronald-kaback et al., Crystal structure of lactose permease in complex with an affinity inactivator yields unique insight into sugar recognition, Proceedings of the National Academy of Sciences, vol.108, issue.23, pp.9361-9366, 2011.
DOI : 10.1073/pnas.1105687108