Whooping cough case numbers rise across the UK and US, Nursing Children and Young People, vol.24, issue.7, p.4, 2012. ,
DOI : 10.7748/ncyp.24.7.4.s2
Pertussis has re-emerged, Ir Med J, vol.105, p.260, 2012. ,
Towards selective inhibitors of adenylyl cyclase toxin from Bordetella pertussis, Trends in Microbiology, vol.20, issue.7, pp.343-351, 2012. ,
DOI : 10.1016/j.tim.2012.04.002
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
Structural basis for the interaction of Bordetella pertussis adenylyl cyclase toxin with calmodulin, The EMBO Journal, vol.14, issue.18 ,
DOI : 10.1016/S0022-2836(03)00271-7
Adenylate Cyclase Toxin, Biochemistry, vol.49, issue.2, pp.318-328, 2010. ,
DOI : 10.1021/bi9016389
URL : https://hal.archives-ouvertes.fr/hal-00512114
Insight into the activation mechanism of Bordetella pertussis adenylate cyclase by calmodulin using fluorescence spectroscopy, European Journal of Biochemistry, vol.10, issue.Suppl., pp.821-833, 2004. ,
DOI : 10.1111/j.1432-1033.2004.03987.x
URL : https://hal.archives-ouvertes.fr/pasteur-00166965
Differential role of calmodulin and calcium ions in the stabilization of the catalytic domain of adenyl cyclase CyaA from Bordetella pertussis, Proteins: Structure, Function, and Bioinformatics, vol.38, issue.5.6, pp.1028-1040, 2012. ,
DOI : 10.1002/prot.24005
Exploring the role of structure and dynamics in the function of chymotrypsin inhibitor 2, Proteins: Structure, Function, and Bioinformatics, vol.322, issue.3, pp.916-924, 2011. ,
DOI : 10.1002/prot.22930
Enhanced internal dynamics of a membrane transport protein during substrate translocation, Protein Science, vol.270, issue.11, pp.2246-2250, 2000. ,
DOI : 10.1110/ps.9.11.2246
Functional Modes and Residue Flexibility Control the Anisotropic Response of Guanylate Kinase to Mechanical Stress, Biophysical Journal, vol.99, issue.10, pp.3412-3419, 2010. ,
DOI : 10.1016/j.bpj.2010.09.026
URL : https://hal.archives-ouvertes.fr/hal-00602505
The role of conformational entropy in molecular recognition by calmodulin, Nature Chemical Biology, vol.50, issue.5, pp.352-358, 2010. ,
DOI : 10.1038/nchembio.347
Protein Flexibility and Enzymatic Catalysis, Adv Protein Chem Struct Biol, vol.87, pp.181-218, 2012. ,
DOI : 10.1016/B978-0-12-398312-1.00007-X
Evolutionarily Conserved Linkage between Enzyme Fold, Flexibility, and Catalysis, PLoS Biology, vol.43, issue.1, p.1001193, 2011. ,
DOI : 10.1371/journal.pbio.1001193.s029
Dynamics and dissipation in enzyme catalysis, Proceedings of the National Academy of Sciences, vol.108, issue.39, pp.16159-16163, 2011. ,
DOI : 10.1073/pnas.1106397108
A Dynamic Knockout Reveals That Conformational Fluctuations Influence the Chemical Step of Enzyme Catalysis, Science, vol.332, issue.6026, pp.234-238, 2011. ,
DOI : 10.1126/science.1198542
Long-timescale molecular dynamics simulations of protein structure and function, Current Opinion in Structural Biology, vol.19, issue.2, pp.120-127, 2009. ,
DOI : 10.1016/j.sbi.2009.03.004
: Throwing Ropes Over Rough Mountain Passes, in the Dark, Annual Review of Physical Chemistry, vol.53, issue.1, pp.291-318, 2002. ,
DOI : 10.1146/annurev.physchem.53.082301.113146
A method for determining reaction paths in large molecules: Application to myoglobin, Chemical Physics Letters, vol.139, issue.5, pp.375-380, 1987. ,
DOI : 10.1016/0009-2614(87)80576-6
dissociative adsorption: Evaluation of free energy barriers in multidimensional quantum systems, Physical Review Letters, vol.72, issue.7, pp.1124-1127, 1994. ,
DOI : 10.1103/PhysRevLett.72.1124
String method in collective variables: Minimum free energy paths and isocommittor surfaces, The Journal of Chemical Physics, vol.125, issue.2, p.24106, 2006. ,
DOI : 10.1063/1.2212942
Markovian milestoning with Voronoi tessellations, The Journal of Chemical Physics, vol.130, issue.19, 2009. ,
DOI : 10.1063/1.3129843
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, issue.3, pp.252-261, 1992. ,
DOI : 10.1016/0009-2614(92)85543-J
Transition-Path Theory and Path-Finding Algorithms for the Study of Rare Events, Annu Rev Phys Chem, vol.61, pp.391-420, 2010. ,
Local elevation: A method for improving the searching properties of molecular dynamics simulation, Journal of Computer-Aided Molecular Design, vol.29, issue.6, pp.695-708, 1994. ,
DOI : 10.1007/BF00124016
Predicting slow structural transitions in macromolecular systems: Conformational flooding, Physical Review E, vol.52, issue.3, pp.2893-2906, 1995. ,
DOI : 10.1103/PhysRevE.52.2893
Escaping free-energy minima, Proceedings of the National Academy of Sciences, vol.99, issue.20, pp.12562-12566, 2002. ,
DOI : 10.1073/pnas.202427399
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC130499
A self-learning algorithm for biased molecular dynamics, Proceedings of the National Academy of Sciences, vol.107, issue.41, pp.17509-17514, 2010. ,
DOI : 10.1073/pnas.1011511107
Accelerated molecular dynamics: A promising and efficient simulation method for biomolecules, The Journal of Chemical Physics, vol.120, issue.24, pp.11919-11929, 2004. ,
DOI : 10.1063/1.1755656
Accessing a Hidden Conformation of the Maltose Binding Protein Using Accelerated Molecular Dynamics, PLoS Computational Biology, vol.49, issue.3 ,
DOI : 10.1371/journal.pcbi.1002034.t002
Targeted Molecular Dynamics Simulation of Conformational Change-Application to the T ??? R Transition in Insulin, Molecular Simulation, vol.264, issue.2-6, pp.291-308, 1993. ,
DOI : 10.1146/annurev.bb.17.060188.002315
Single-Molecule Experiments in Vitro and in Silico, Science, vol.316, issue.5828, pp.1144-1148, 2007. ,
DOI : 10.1126/science.1137591
A temperature accelerated method for sampling free energy and determining reaction pathways in rare events simulations, Chemical Physics Letters, vol.426, issue.1-3 ,
DOI : 10.1016/j.cplett.2006.05.062
New Monte Carlo technique for studying phase transitions, Physical Review Letters, vol.61, issue.23, pp.2635-2638, 1988. ,
DOI : 10.1103/PhysRevLett.61.2635
Single-sweep methods for free energy calculations, The Journal of Chemical Physics, vol.128, issue.18, p.184110, 2008. ,
DOI : 10.1063/1.2907241
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
Calculations of free energy barriers for local mechanisms of hydrogen diffusion in alanates, Scientific Modeling and Simulation SMNS, vol.126, issue.1-3, p.187, 2008. ,
DOI : 10.1007/s10820-008-9097-x
by Ab Initio Rare Event Simulations, The Journal of Physical Chemistry C, vol.116, issue.37, pp.19636-19643, 2012. ,
DOI : 10.1021/jp3019588
URL : https://hal.archives-ouvertes.fr/hal-01498114
A Computational Study of Water and CO Migration Sites and Channels Inside Myoglobin, Journal of Chemical Theory and Computation, vol.9, issue.2, pp.1265-1271, 2013. ,
DOI : 10.1021/ct300862j
Temperature accelerated Monte Carlo (TAMC): a method for sampling the free energy surface of non-analytical collective variables, Physical Chemistry Chemical Physics, vol.41, issue.13, pp.5952-5959, 2011. ,
DOI : 10.1039/c0cp01335h
On-the-fly free energy parameterization via temperature accelerated molecular dynamics, Chemical Physics Letters, vol.547, pp.114-119, 2012. ,
DOI : 10.1016/j.cplett.2012.07.064
MuSTAR MD: Multi-scale sampling using temperature accelerated and replica exchange molecular dynamics, The Journal of Chemical Physics, vol.139, issue.14, pp.145105-145115, 2013. ,
DOI : 10.1063/1.4823743
Probing the Structures of Hydrated Nafion in Different Morphologies Using Temperature-Accelerated Molecular Dynamics Simulations, The Journal of Physical Chemistry C, vol.117, issue.2, 2012. ,
DOI : 10.1021/jp309038n
Large-scale conformational sampling of proteins using temperature-accelerated molecular dynamics, Proceedings of the National Academy of Sciences, vol.107, issue.11, pp.4961-4966, 2010. ,
DOI : 10.1073/pnas.0914540107
"DFG-flip" in the Insulin Receptor Kinase is Facilitated by a Helical Intermediate State of the Activation Loop, Biophysical Journal, vol.100, issue.3, pp.1979-1987, 2012. ,
DOI : 10.1016/j.bpj.2010.12.3112
Conformational Sampling of Maltose-Transporter Components in Cartesian Collective Variables Is Governed by the Low-Frequency Normal Modes, The Journal of Physical Chemistry Letters, vol.3, issue.22, pp.3379-3384, 2012. ,
DOI : 10.1021/jz301650q
The Dynamic Process of ??2-Adrenergic Receptor Activation, Cell, vol.152, issue.3, pp.532-542, 2013. ,
DOI : 10.1016/j.cell.2013.01.008
All-atom structural models of insulin binding to the insulin receptor in the presence of a tandem hormone-binding element, Proteins: Structure, Function, and Bioinformatics, vol.479, issue.suppl. 2, pp.1017-1030, 2013. ,
DOI : 10.1002/prot.24255
Extending the Generality of Molecular Dynamics Simulations on a Special-Purpose Machine, 2013 IEEE 27th International Symposium on Parallel and Distributed Processing, pp.933-945, 2013. ,
DOI : 10.1109/IPDPS.2013.93
Conformational Dynamics of a Regulator of G-Protein Signaling Protein Reveals a Mechanism of Allosteric Inhibition by a Small Molecule, ACS Chemical Biology, vol.8, issue.12, 2013. ,
DOI : 10.1021/cb400568g
Comparative Protein Structure Modeling using Modeller, Current Protocols in Bioinformatics, vol.5, pp.5-6, 2006. ,
Extending the treatment of backbone energetics in protein force fields: Limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations, Journal of Computational Chemistry, vol.44, issue.Pt 6 Pt 1, pp.1400-1415, 2004. ,
DOI : 10.1002/jcc.20065
All-atom empirical potential for molecular modeling and dynamics studies of proteins, J Phys Chem B, vol.102, pp.3586-3616, 1998. ,
Comparison of simple potential functions for simulating liquid water, The Journal of Chemical Physics, vol.79, issue.2, pp.926-935, 1983. ,
DOI : 10.1063/1.445869
Scalable molecular dynamics with NAMD, Journal of Computational Chemistry, vol.84, issue.16, pp.1781-1802, 2005. ,
DOI : 10.1002/jcc.20289
Particle Mesh Ewald and an N.log(N) method for Ewald sums in large systems, J Chem Phys, vol.98, pp.3684-90, 1993. ,
Understanding Molecular Simulation, Computers in Physics, vol.11, issue.4, 2002. ,
DOI : 10.1063/1.4822570
Constant pressure molecular dynamics algorithms, The Journal of Chemical Physics, vol.101, issue.5, pp.4177-4189, 1994. ,
DOI : 10.1063/1.467468
Constant pressure molecular dynamics simulation: The Langevin piston method, The Journal of Chemical Physics, vol.103, issue.11, pp.4613-4622, 1995. ,
DOI : 10.1063/1.470648
Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes, Journal of Computational Physics, vol.23, issue.3, pp.327-341, 1977. ,
DOI : 10.1016/0021-9991(77)90098-5
Rattle: A ???velocity??? version of the shake algorithm for molecular dynamics calculations, Journal of Computational Physics, vol.52, issue.1, pp.24-34, 1983. ,
DOI : 10.1016/0021-9991(83)90014-1
Ensemble-Based Convergence Analysis of Biomolecular Trajectories, Biophysical Journal, vol.91, issue.1, pp.164-172, 2006. ,
DOI : 10.1529/biophysj.106.082941
The Amber biomolecular simulation programs, Journal of Computational Chemistry, vol.124, issue.16, pp.1668-1688, 2005. ,
DOI : 10.1002/jcc.20290
PiSQRD: a web server for decomposing proteins into quasi-rigid dynamical domains, Bioinformatics, vol.25, issue.20, pp.2743-2744, 2009. ,
DOI : 10.1093/bioinformatics/btp512
Coarse-Grained Description of Protein Internal Dynamics: An Optimal Strategy for Decomposing Proteins in Rigid Subunits, Biophysical Journal, vol.96, issue.12, pp.4993-5002, 2009. ,
DOI : 10.1016/j.bpj.2009.03.051
Knowledge-based protein secondary structure assignment, Proteins: Structure, Function, and Genetics, vol.206, issue.4, pp.566-579, 1995. ,
DOI : 10.1002/prot.340230412
The terahertz dance of water with the proteins: the effect of protein flexibility on the dynamical hydration shell of ubiquitin, Faraday Discuss., vol.14, pp.161-173, 2009. ,
DOI : 10.1039/B804734K
Sitting at the Edge: How Biomolecules use Hydrophobicity to Tune Their Interactions and Function, The Journal of Physical Chemistry B, vol.116, issue.8, pp.2498-2503, 2012. ,
DOI : 10.1021/jp2107523