The design of molecular hosts, guests, and their complexes (nobel lecture, Angewandte Chemie International Edition in English, vol.27, issue.8, pp.1009-1020, 1988. ,
Supramolecular chemistry-scope and perspectives molecules, supermolecules, and molecular devices (nobel lecture, Angewandte Chemie International Edition in English, vol.27, issue.1, pp.89-112, 1988. ,
DOI : 10.1002/anie.198800891
The discovery of crown ethers (noble lecture, Angewandte Chemie International Edition in English, vol.27, issue.8, pp.1021-1027, 1988. ,
Using self-assembly for the fabrication of nano-scale electronic and photonic devices, IEEE transactions on advanced packaging, vol.26, pp.233-241, 2003. ,
The principles of quantum mechanics, vol.27, 1981. ,
The theory of intermolecular forces, 2013. ,
From supramolecular chemistry towards constitutional dynamic chemistry and adaptive chemistry, Chemical Society Reviews, vol.36, issue.2, pp.151-160, 2007. ,
URL : https://hal.archives-ouvertes.fr/hal-00680548
Cooperativity theory in biochemistry: steadystate and equilibrium systems, 1985. ,
An introduction to statistical thermodynamics. Courier Corporation, 2012. ,
DOI : 10.1063/1.3057470
Negative cooperativity in regulatory enzymes, Proceedings of the National Academy of Sciences, vol.62, pp.1121-1128, 1969. ,
Basics of molecular recognition, 2016. ,
Molecular recognition: from solution science to nano/-materials technology, Chemical Society Reviews, vol.41, issue.17, pp.5800-5835, 2012. ,
Bond dissociation energies of organic molecules, Accounts of chemical research, vol.36, issue.4, pp.255-263, 2003. ,
Definition and emergence of supramolecular chemistry, 2012. ,
Predicting binding free energies: Frontiers and benchmarks, Annual Review of Biophysics, vol.46, pp.531-558, 2017. ,
The sampl4 host-guest blind prediction challenge: an overview, Journal of computeraided molecular design, vol.28, issue.4, pp.305-317, 2014. ,
Overview of the sampl5 host-guest challenge: Are we doing better?, Journal of computer-aided molecular design, vol.31, issue.1, pp.1-19, 2017. ,
Overview of the sampl6 host-guest binding affinity prediction challenge, p.371724, 2018. ,
D3r grand challenge 2: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies, Journal of computer-aided molecular design, vol.32, issue.1, pp.1-20, 2018. ,
Hydrophobe challenge: A joint experimental and computational study on the host-guest binding of hydrocarbons to cucurbiturils, allowing explicit evaluation of guest hydration free-energy contributions, The Journal of Physical Chemistry B, vol.121, issue.49, pp.11144-11162, 2017. ,
Cucurbituril-based molecular recognition, 2015. ,
Complexation thermodynamics of cyclodextrins, Chemical reviews, vol.98, issue.5, pp.1875-1918, 1998. ,
Ligand binding thermodynamics in drug discovery: still a hot tip?, Journal of medicinal chemistry, vol.58, issue.16, pp.6321-6335, 2015. ,
Isothermal titration calorimetry in drug discovery, Progress in medicinal chemistry, vol.38, pp.309-376, 2001. ,
Statistical Mechanics, 1976. ,
Allosteric mechanisms of signal transduction, Science, vol.308, issue.5727, pp.1424-1428, 2005. ,
Exploring the role of receptor flexibility in structure-based drug discovery, Biophysical chemistry, vol.186, pp.31-45, 2014. ,
Frontiers in free-energy calculations of biological systems, Wiley Interdisciplinary Reviews: Computational Molecular Science, vol.4, pp.71-89, 2014. ,
Free energy calculations: applications to chemical and biochemical phenomena, Chemical reviews, vol.93, pp.2395-2417, 1993. ,
,
How to improve r&d productivity: the pharmaceutical industry's grand challenge, Nature reviews Drug discovery, vol.9, issue.3, pp.203-214, 2010. ,
The cost of drug development: a systematic review, Health Policy, vol.100, issue.1, pp.4-17, 2011. ,
Binding free energy calculations for lead optimization: assessment of their accuracy in an industrial drug design context, Journal of chemical theory and computation, vol.10, issue.8, pp.3331-3344, 2014. ,
Efficient computation of absolute free energies of binding by computer simulations. application to the methane dimer in water, The Journal of chemical physics, vol.89, issue.6, pp.3742-3746, 1988. ,
Inclusion of loss of translational and rotational freedom in theoretical estimates of free energies of binding. application to a complex of benzene and mutant t4 lysozyme, Journal of the American Chemical Society, vol.119, issue.11, pp.2707-2714, 1997. ,
Absolute binding free energies: a quantitative approach for their calculation, The Journal of Physical Chemistry B, vol.107, issue.35, pp.9535-9551, 2003. ,
The statistical-thermodynamic basis for computation of binding affinities: a critical review, Biophysical journal, vol.72, issue.3, p.1047, 1997. ,
Free energy calculations: a breakthrough for modeling organic chemistry in solution, Accounts of Chemical Research, vol.22, issue.5, pp.184-189, 1989. ,
Calculation of absolute protein-ligand binding free energy from computer simulations, Proceedings of the National Academy of Sciences of the United States of America, vol.102, pp.6825-6830, 2005. ,
Calculation of absolute protein-ligand binding affinity using path and endpoint approaches, Biophysical journal, vol.90, issue.3, pp.864-877, 2006. ,
Fast and accurate predictions of binding free energies using MM-PBSA and MM-GBSA", Journal of computational chemistry, vol.31, issue.4, pp.797-810, 2010. ,
Protein structural change upon ligand binding: linear response theory, Physical review letters, vol.94, issue.7, p.78102, 2005. ,
DOI : 10.1103/physrevlett.94.078102
Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models, Accounts of Chemical Research, vol.33, issue.12, pp.889-897, 2000. ,
Continuum solvent studies of the stability of dna, rna, and phosphoramidatedna helices, Journal of the American Chemical Society, vol.120, issue.37, pp.9401-9409, 1998. ,
A new method for predicting binding affinity in computer-aided drug design, Protein engineering, vol.7, issue.3, pp.385-391, 1994. ,
Linear interaction energy: method and applications in drug design, Computational Drug Discovery and Design, pp.305-323, 2012. ,
Docking and scoring in virtual screening for drug discovery: methods and applications, Nature reviews Drug discovery, vol.3, issue.11, pp.935-949, 2004. ,
Pairwise GB/SA scoring function for structure-based drug design, The Journal of Physical Chemistry B, vol.108, issue.17, pp.5453-5462, 2004. ,
DOI : 10.1021/jp0312518
Accurate calculation of conformational free energy differences in explicit water: The confinement-solvation free energy approach, The Journal of Physical Chemistry B, vol.119, issue.16, pp.5194-5207, 2015. ,
Free energy simulations come of age: protein-ligand recognition, Accounts of chemical research, vol.35, issue.6, pp.430-437, 2002. ,
Good practices in free-energy calculations, The Journal of Physical Chemistry B, vol.114, issue.32, pp.10235-10253, 2010. ,
Standard binding free energies from computer simulations: What is the best strategy?, Journal of chemical theory and computation, vol.9, issue.1, pp.794-802, 2012. ,
Absolute binding free energy calculations using molecular dynamics simulations with restraining potentials, Biophysical journal, vol.91, issue.8, pp.2798-2814, 2006. ,
The hidden energetics of ligand binding and activation in a glutamate receptor, Nature structural & molecular biology, vol.18, issue.3, pp.283-287, 2011. ,
Efficient determination of protein-protein standard binding free energies from first principles, Journal of chemical theory and computation, vol.9, issue.8, pp.3789-3798, 2013. ,
Accurate and reliable prediction of relative ligand binding potency in prospective drug discovery by way of a modern freeenergy calculation protocol and force field, vol.137, pp.2695-2703, 2015. ,
Harmonic dynamics of proteins: normal modes and fluctuations in bovine pancreatic trypsin inhibitor, Proceedings of the National Academy of Sciences, vol.80, pp.6571-6575, 1983. ,
Quantum corrections to the free energy difference between peptides and proteins conformers, Journal of chemical theory and computation, vol.11, issue.9, pp.4011-4022, 2015. ,
Evaluation of the configurational entropy for proteins: application to molecular dynamics simulations of an ?-helix, Macromolecules, vol.17, issue.7, pp.1370-1374, 1984. ,
Method for estimating the configurational entropy of macromolecules, Macromolecules, vol.14, issue.2, pp.325-332, 1981. ,
Converging free energy estimates: MM-PB(GB)SA studies on the protein-protein complex ras-raf, Journal of computational chemistry, vol.25, issue.2, pp.238-250, 2004. ,
Comparison of end-point continuum-solvation methods for the calculation of protein-ligand binding free energies, Proteins: Structure, Function, and Bioinformatics, vol.80, pp.1326-1342, 2012. ,
Assessing the performance of the MM/PBSA and MM/G-BSA methods. 1. the accuracy of binding free energy calculations based on molecular dynamics simulations, Journal of chemical information and modeling, vol.51, issue.1, pp.69-82, 2010. ,
Assessing the performance of the MM/PBSA and MM/G-BSA methods: Ii. the accuracy of ranking poses generated from docking, Journal of computational chemistry, vol.32, issue.5, p.866, 2011. ,
Assessing the performance of MM/PBSA and MM/G-BSA methods. 4. accuracies of MM/PBSA and MM/GBSA methodologies evaluated by various simulation protocols using pdbbind data set, Physical Chemistry Chemical Physics, vol.16, issue.31, pp.16719-16729, 2014. ,
An MM/3D-RISM approach for ligand binding affinities, The Journal of Physical Chemistry B, vol.114, issue.25, pp.8505-8516, 2010. ,
Assessing the performance of MM/PBSA and MM/G-BSA methods. 3. the impact of force fields and ligand charge models, The Journal of Physical Chemistry B, vol.117, issue.28, pp.8408-8421, 2013. ,
Accounting for ligand conformational restriction in calculations of protein-ligand binding affinities, Biophysical journal, vol.98, issue.5, pp.901-910, 2010. ,
The normal-mode entropy in the MM/GBSA method: effect of system truncation, buffer region, and dielectric constant, Journal of chemical information and modeling, vol.52, issue.8, pp.2079-2088, 2012. ,
QM/MM-PBSA method to estimate free energies for reactions in proteins, The Journal of Physical Chemistry B, vol.112, issue.39, pp.12537-12548, 2008. ,
Calculations of antibody-antigen interactions: microscopic and semi-microscopic evaluation of the free energies of binding of phosphorylcholine analogs to mcpc603, Protein Engineering, vol.5, issue.3, pp.215-228, 1992. ,
Chemical and electrochemical electron-transfer theory, Annual Review of Physical Chemistry, vol.15, issue.1, pp.155-196, 1964. ,
DOI : 10.1146/annurev.pc.15.100164.001103
Solvation thermodynamics of nonionic solutes, The Journal of chemical physics, vol.81, issue.4, pp.2016-2027, 1984. ,
Improving the accuracy of the linear interaction energy method for solvation free energies, Journal of chemical theory and computation, vol.3, issue.6, pp.2162-2175, 2007. ,
The linear interaction energy method for predicting ligand binding free energies, Combinatorial chemistry & high throughput screening, vol.4, pp.613-626, 2001. ,
On the validity of electrostatic linear response in polar solvents, The Journal of Physical Chemistry, vol.100, issue.22, pp.9512-9521, 1996. ,
Efficient evaluation of binding free energy using continuum electrostatics solvation, Journal of medicinal chemistry, vol.47, issue.23, pp.5791-5797, 2004. ,
DOI : 10.1021/jm049726m
Library screening by fragment-based docking, Journal of Molecular Recognition, vol.23, issue.2, pp.183-193, 2010. ,
DOI : 10.1002/jmr.981
URL : http://www.zora.uzh.ch/id/eprint/23623/2/Huang_J_Mol_Recognit_2009.pdf
Is quantum mechanics necessary for predicting binding free energy?, Journal of medicinal chemistry, vol.51, issue.14, pp.4280-4288, 2008. ,
DOI : 10.1021/jm800242q
Quantum mechanical methods for drug design, Current topics in medicinal chemistry, vol.10, pp.33-45, 2010. ,
DOI : 10.2174/156802610790232242
URL : http://www.zora.uzh.ch/id/eprint/25391/1/Zhou_Curr_Top_Med_2009_V.pdf
Virtual screening of drugs: score functions, docking, and drug design, Current Computer-Aided Drug Design, vol.4, issue.4, pp.265-272, 2008. ,
Scoring functions and their evaluation methods for protein-ligand docking: recent advances and future directions, Physical Chemistry Chemical Physics, vol.12, issue.40, pp.12899-12908, 2010. ,
DOI : 10.1039/c0cp00151a
Prediction of binding constants of protein ligands: a fast method for the prioritization of hits obtained from de novo design or 3d database search programs, Journal of computeraided molecular design, vol.12, issue.4, pp.309-309, 1998. ,
Predicting binding affinities of protein ligands from three-dimensional models: application to peptide binding to class i major histocompatibility proteins, Journal of medicinal chemistry, vol.42, issue.22, pp.4650-4658, 1999. ,
Automated docking with grid-based energy evaluation, Journal of computational chemistry, vol.13, issue.4, pp.505-524, 1992. ,
DOI : 10.1002/jcc.540130412
Autodock4 and autodocktools4: Automated docking with selective receptor flexibility, Journal of computational chemistry, vol.30, issue.16, pp.2785-2791, 2009. ,
DOI : 10.1002/jcc.21256
URL : https://onlinelibrary.wiley.com/doi/pdf/10.1002/jcc.21256
host-guest chemistry". Annual Reports Section" B, vol.85, pp.353-386, 1988. ,
Cucurbituril homologues and derivatives: new opportunities in supramolecular chemistry, Accounts of chemical research, vol.36, issue.8, pp.621-630, 2003. ,
Supramolecular binding thermodynamics by dispersion-corrected density functional theory, Chemistry-A European Journal, vol.18, issue.32, pp.9955-9964, 2012. ,
DOI : 10.1002/chem.201200497
Release of highenergy water as an essential driving force for the high-affinity binding of cucurbit [n] urils", Journal of the American Chemical Society, vol.134, issue.37, pp.15318-15323, 2012. ,
Perspectives in supramolecular chemistry-from molecular recognition towards molecular information processing and selforganization, Angewandte Chemie International Edition in English, vol.29, issue.11, pp.1304-1319, 1990. ,
Application of molecular recognition technology to green chemistry: Analytical determinations of metals in metallurgical, environmental, waste, and radiochemical samples, Metal Sustainability: Global Challenges, Consequences, and Prospects, p.271, 2016. ,
Synthetic mimics of biotin/(strept) avidin, Chemical Society Reviews, vol.46, issue.9, pp.2391-2403, 2017. ,
Pillar-shaped macrocyclic hosts pillar [n] arenes: new key players for supramolecular chemistry, Chem. Rev, issue.14, pp.7937-8002, 2016. ,
DOI : 10.1021/acs.chemrev.5b00765
Predicting accurate absolute binding energies in aqueous solution: thermodynamic considerations for electronic structure methods, Physical Chemistry Chemical Physics, vol.17, issue.19, pp.12441-12451, 2015. ,
Computational approaches to the chemical equilibrium constant in proteinligand binding, Molecular Informatics, vol.35, pp.555-567, 2016. ,
Implicit solvent models, Biophysical chemistry, vol.78, issue.1-2, pp.1-20, 1999. ,
DOI : 10.1201/9780203903827.ch7
Cucurbiturils: from synthesis to high-affinity binding and catalysis, Chemical Society Reviews, vol.44, issue.2, pp.394-418, 2015. ,
DOI : 10.1039/c4cs00273c
URL : https://pubs.rsc.org/en/content/articlepdf/2015/cs/c4cs00273c
Development and testing of a general amber force field, Journal of computational chemistry, vol.25, issue.9, pp.1157-1174, 2004. ,
Cyclodextrins and their pharmaceutical applications, International journal of pharmaceutics, vol.329, issue.1, pp.1-11, 2007. ,
Charmm general force field: A force field for druglike molecules compatible with the charmm allatom additive biological force fields, Journal of Computational Chemistry, vol.31, issue.4, pp.671-690, 2010. ,
Nanomolar binding of steroids to cucurbit [n] urils: selectivity and applications, Journal of the American Chemical Society, vol.138, issue.39, pp.13022-13029, 2016. ,
DOI : 10.1021/jacs.6b07655
Calculation of host-guest binding affinities using a quantummechanical energy model, Journal of chemical theory and computation, vol.8, issue.6, pp.2023-2033, 2012. ,
The cambridge structural database, Acta Crystallographica Section B: Structural Science, Crystal Engineering and Materials, vol.72, issue.2, pp.171-179, 2016. ,
Marvinsketch, 2014. ,
Plants: Application of ant colony optimization to structurebased drug design, pp.247-258, 2006. ,
Fast, efficient generation of high-quality atomic charges. am1-bcc model: I. method, Journal of Computational Chemistry, vol.21, issue.2, pp.132-146, 2000. ,
Gromacs: High performance molecular simulations through multilevel parallelism from laptops to supercomputers, pp.19-25, 2015. ,
Canonical sampling through velocity rescaling, The Journal of chemical physics, vol.126, p.14101, 2007. ,
DOI : 10.1063/1.2408420
URL : http://arxiv.org/pdf/0803.4060
Constant pressure molecular dynamics algorithms, The Journal of Chemical Physics, vol.101, issue.5, pp.4177-4189, 1994. ,
DOI : 10.1063/1.467468
Strain fluctuations and elastic constants, The Journal of Chemical Physics, vol.76, issue.5, pp.2662-2666, 1982. ,
DOI : 10.1063/1.443248
Direct-space corrections enable fast and accurate lorentz-berthelot combination rule lennard-jones lattice summation, Journal of chemical theory and computation, vol.11, issue.12, pp.5737-5746, 2015. ,
Computational drug discovery and design, 2012. ,
The amber biomolecular simulation programs, Journal of computational chemistry, vol.26, issue.16, pp.1668-1688, 2005. ,
DOI : 10.1002/jcc.20290
URL : http://europepmc.org/articles/pmc1989667?pdf=render
, , 2017.
Parametrized models of aqueous free energies of solvation based on pairwise descreening of solute atomic charges from a dielectric medium, The Journal of Physical Chemistry, vol.100, issue.51, pp.19824-19839, 1996. ,
Hydrogen bonding in organic synthesis, 2009. ,
Proton transfer, acid-base catalysis, and enzymatic hydrolysis. part i: Elementary processes, Angewandte Chemie International Edition in English, vol.3, issue.1, pp.1-19, 1964. ,
DOI : 10.1002/anie.196400011
designer acids": combined acid catalysis for asymmetric synthesis ,
DOI : 10.1002/anie.200460394
, Angewandte Chemie International Edition, vol.44, issue.13, pp.1924-1942, 2005.
Single-centered hydrogen-bonded enhanced acidity (shea) acids: a new class of brønsted acids, Journal of the American Chemical Society, vol.131, issue.46, pp.16984-16988, 2009. ,
Kinetics and mechanisms of addition of acids to olefins. part i. the addition of hydrogen chloride to isobutene in nitromethane, Journal of the Chemical Society, pp.1292-1297, 1960. ,
Kinetics and mechanism of addition of acids to olefins. iii. addition of hydrogen chloride to 2-methyl-1-butene, 2-methyl-2-butene, and isoprene in nitromethane, Journal of the American Chemical Society, vol.91, issue.15, pp.4199-4205, 1969. ,
Kinetics and mechanism of addition of acids to olefins. iv. addition of hydrogen and deuterium chloride to 3-methyl-1-butene, 3, 3-dimethyl-1-butene, 1-methylcyclopentene, and 1-methylcyclopentene-2, 5, 5-d3, Journal of the American Chemical Society, vol.91, issue.15, pp.4205-4210, 1969. ,
Nitro-assisted brønsted acid catalysis: Application to a challenging catalytic azidation, Journal of the American Chemical Society, vol.137, issue.30, pp.9555-9558, 2015. ,
DOI : 10.1021/jacs.5b06055
Long-range corrected hybrid density functionals with damped atom-atom dispersion corrections, Physical Chemistry Chemical Physics, vol.10, issue.44, pp.6615-6620, 2008. ,
DOI : 10.1039/b810189b
URL : https://digital.library.unt.edu/ark:/67531/metadc929924/m2/1/high_res_d/949212.pdf
Avogadro: an advanced semantic chemical editor, visualization, and analysis platform, Journal of cheminformatics, vol.4, issue.1, p.17, 2012. ,
DOI : 10.1186/1758-2946-4-17
URL : https://doi.org/10.1186/1758-2946-4-17
Low-cost quantum chemical methods for noncovalent interactions, The journal of physical chemistry letters, vol.5, issue.24, pp.4275-4284, 2014. ,
DOI : 10.1021/jz5021313
URL : https://doi.org/10.1021/jz5021313
The orca program system, Wiley Interdisciplinary Reviews: Computational Molecular Science, vol.2, issue.1, pp.73-78, 2012. ,
, Gaussian, vol.09, 2009.
Principles of qsar models validation: internal and external, QSAR & combinatorial science, vol.26, issue.5, pp.694-701, 2007. ,