K. Raghavachari and A. Saha, Accurate Composite and Fragment-Based Quantum Chemical Models for Large Molecules, Chem. Rev, vol.115, pp.5643-5677, 2015.

J. Gao, Hybrid Quantum and Molecular Mechanical Simulations: An Alternative Avenue to Solvent Effects in Organic Chemistry, Acc. Chem. Res, vol.29, pp.298-305, 1996.

J. Gao, Methods and Applications of Combined Quantum Mechanical and Molecular Mechanical Potentials, In Reviews in Computational Chemistry, vol.7, pp.119-186, 1996.

H. M. Senn and W. Thiel, QM/MM Methods for Biomolecular Systems, Angew. Chem., Int. Ed, vol.48, pp.1198-1229, 2009.

T. A. Wesolowski, S. Shedge, and X. Zhou, Frozen-Density Embedding Strategy for Multilevel Simulations of Electronic Structure, Chem. Rev, vol.115, pp.5891-5928, 2015.

W. Yang, Direct Calculation of electron Density in Density-Functional Theory, Phys. Rev. Lett, vol.66, pp.1438-1441, 1991.

W. Yang, Direct Calculation of Electron Density in density-Functional Theory: Implementation for Benzene and a Tetrapeptide, Phys. Rev. A, vol.44, pp.7823-7826, 1991.

W. Yang and T. Lee, A density-Matrix Divide-and-Conquer Approach for Electronic Structure Calculations of Large Molecules, J. Chem. Phys, vol.103, pp.5674-5678, 1995.

S. L. Dixon, K. M. Merz, and . Jr, Semiempirical Molecular Orbital Calculations with Linear System Size Scaling, J. Chem. Phys, vol.104, pp.6643-6649, 1996.

S. L. Dixon, K. M. Merz, . Jr, and . Fast, Accurate Semiempirical Molecular Orbital Calculations for Macromolecules, J. Chem. Phys, vol.107, pp.879-893, 1997.

V. Gogonea, L. M. Westerhoff, K. M. Merz, and . Jr, Quantum Mechanical/Quantum Mechanical Methods. I. A Divide and Conquer Strategy for Solving the Schrödinger Equation for Large Molecular Systems Using a Composite Density Functional-Semiempirical Hamiltonian, J. Chem. Phys, vol.113, pp.5604-5613, 2000.

X. He, K. M. Merz, and . Jr, Divide and Conquer Hartree-Fock Calculations on Proteins, J. Chem. Theory Comput, vol.6, pp.405-411, 2010.

D. W. Zhang and J. Z. Zhang, Molecular Fractionation with Conjugate Caps for Full Quantum Mechanical Calculation of Protein-Molecule Interaction Energy, J. Chem. Phys, vol.119, pp.3599-3605, 2003.

Y. Mey, D. W. Zhang, and J. Z. Zhang, New Method for Direct Linear-Scaling Calculation of Electron Density of Proteins, J. Phys. Chem. A, vol.109, pp.2-5, 2005.

X. He and J. Z. Zhang, A New Method for Direct Calculation of Total Energy of Protein, J. Chem. Phys, vol.122, p.31103, 2005.

X. He and J. Z. Zhang, The Generalized Molecular Fractionation with Conjugate Caps/Molecular Mechanics Method for Direct Calculation of Protein Energy, J. Chem. Phys, vol.124, p.184703, 2006.

K. Babu and S. R. Gadre, Ab Initio Quality One-Electron Properties of Large Molecules: Development and Testing of Molecular Yailoring Approach, J. Comput. Chem, vol.24, pp.484-495, 2003.

V. Ganesh, R. K. Dongare, P. Balanarayan, and S. R. Gadre, Molecular Tailoring Approach for Geometry Optimization of Large Molecules: Energy Evaluation and Parallelization Strategies, J. Chem. Phys, p.125, 2006.

N. Sahu and S. R. Gadre, Molecualr Tailoring Approach: A Route for Ab Initio Treatment of Large Clusters, Acc. Chem. Res, vol.47, pp.2739-2747, 2014.

L. Huang, L. Massa, and J. Karle, Kernel Energy Method Illustrated with Peptides, Int. J. Quantum Chem, vol.103, pp.808-817, 2005.

L. Huang, L. Massa, and J. Karle, Kernel Energy Method: Application to Insulin, Proc. Natl. Acad. Sci, vol.102, pp.12690-12693, 2005.

L. Huang, H. Bohorquez, C. F. Matta, and L. Massa, The Kernel Energy Method: Application to Graphene and Extended Aromatics, Int. J. Quantum Chem, vol.111, pp.4150-4157, 2011.

L. Huang, C. F. Matta, and L. Massa, The Kernel Energy Method (KEM) Delivers Fast and Accurate QTAIM Electrostatic Charge for Atoms in Large Molecules, Struct. Chem, vol.26, pp.1433-1442, 2015.

M. Svensson, S. Humbel, R. D. Froese, T. Matsubara, S. Sieber et al., ONIOM: A Multilayered Integrated MO+MM Method for Geometry Optimizations and Single Point Energy Predictions. A Test for Diels-Alder Reactions and

, Oxidative Addition. J. Phys. Chem, vol.100, pp.19357-19363, 1996.

S. Humbel, S. Sieber, and K. Morokuma, The IMOMO Method: Integration of Different Levels of Molecular Orbital Approximations for Geometry Optimization of Large Systems: Test for n-Butane Conformation and SN2 Reaction: RCl+Cl ?, J. Chem. Phys, vol.105, pp.1959-1967, 1996.

T. Vreven and K. Morokuma, On the Application of the IMOMO (Integrated Molecular Orbital + Molecular Orbital) method, J. Comput. Chem, vol.21, pp.1419-1432, 2000.

L. W. Chung, W. M. Sameera, R. Ramozzi, A. J. Page, M. Hatanaka et al., The ONIOM Method and Its Application, Chem. Rev, vol.115, pp.5678-5796, 2015.

K. Kitaura, E. Ikeo, T. Asada, T. Nakano, and M. Uebayasi, Fragment Molecular Orbital Method: an Approximate Computational Method for Large Molecules, Chem. Phys. Lett

T. Nakano, T. Kaminuma, T. Sato, Y. Akiyama, M. Uebayasi et al., Fragment Molecular Orbital Method: Application to Polypeptides, Chem. Phys. Lett, vol.318, pp.614-618, 2000.

D. G. Fedorov and K. Kitaura, Theoretical Development of the Fragment Molecular Orbital (FMO) Method, In Modern Methods for Theoretical Physical Chemistry and Biopolymers

E. B. Starikov, J. P. Lewis, and S. Tanaka, , pp.3-38, 2006.

D. G. Fedorov and K. Kitaura, Theoretical Background of the Fragment Molecular Orbital (FMO) Method and Its Implementation in GAMESS. In The Fragment Molecular Orbital Method: Practical Applications to Large Molecular Systems, pp.5-36, 2009.

S. R. Pruitt, C. Bertoni, K. R. Brorsen, and M. S. Gordon, Efficient and Accurate Fragmentation Methods, Acc. Chem. Res, vol.47, pp.2786-2794, 2014.

P. D. Walker and P. G. Mezey, Molecular Electron Density Lego Approach to Molecule Building, J. Am. Chem. Soc, vol.115, pp.12423-12430, 1993.

P. D. Walker and P. G. Mezey, Ab Initio Quality Electron Densities for Proteins: A MEDLA Approach, J. Am. Chem. Soc, vol.116, pp.12022-12032, 1994.

T. E. Exner and P. G. Mezey, Ab Initio-Quality Electrostatic Potentials for Proteins: An Application of the ADMA Approach, J. Phys. Chem. A, vol.106, pp.11791-11800, 2002.

T. E. Exner and P. G. Mezey, Ab Initio Quality Properties for Macromolecules Using the ADMA Approach, J. Comput. Chem, vol.24, pp.1980-1986, 2003.

Z. Szekeres, T. Exner, and P. G. Mezey, Fuzzy Fragment Selection Strategies, Basis Set Dependence and HF-DFT Comparisons in the Applications of the ADMA Method of Macromolecular Quantum Chemistry, Int. J. Quantum Chem, vol.104, pp.847-860, 2005.

B. Meyer, B. Guillot, M. F. Ruiz-lopez, and A. Genoni, Libraries of Extremely Localized Molecular Orbitals. 1. Model Molecules Approximation and Molecular Orbitals Transferability, J. Chem. Theory. Comput, vol.12, pp.1052-1067, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01532026

B. Meyer, B. Guillot, M. F. Ruiz-lopez, C. Jelsch, and A. Genoni, Libraries of Extremely Localized Molecular Orbitals. 2. Comparison with the Pseudoatoms Transferability, J. Chem. Theory. Comput, vol.12, pp.1068-1081, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01532026

B. Meyer and A. Genoni, Libraries of Extremely Localized Molecular Orbitals. 3. Construction and Preliminary Assessment of the New Databanks, J. Phys. Chem. A, vol.122, pp.8965-8981, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01532026

A. Warshel and M. Levitt, Theoretical Studies of Enzymic Reactions: Dielectric, Electrostatic and Steric Stabilization of the Carbonium ion in the Reaction of Lysozyme, J. Mol. Biol, vol.103, pp.227-249, 1976.

M. J. Field, P. A. Bash, and M. Karplus, A Combined Quantum Mechanical and Molecular Mechanical Potential for Molecular Dynamics Simulations, J. Comput Chem, vol.11, pp.700-733, 1990.

T. A. Wesolowski and A. Warshel, Frozen Density Functional Approach for Ab Initio Calculations of Solvated Molecules, J. Phys. Chem, vol.97, pp.8050-8053, 1993.

T. A. Wesolowski, Embedding a Multideterminantal Wave Function in an Orbital-Free Environment, Phys. Rev. A, p.12504, 2008.

K. Pernal and T. A. Wesolowski, Orbital-Free Effective Embedding Potential: Density-Matrix Functional Theory Case, Int. J. Quantum Chem, vol.109, pp.2520-2525, 2009.

R. Poteau, I. Ortega, F. Alary, A. Ramirez-solis, J. Barthelat et al., Effective Group Potentials. 1. Method. J. Phys. Chem. A, vol.105, pp.198-205, 2001.

R. Poteau, F. Alary, H. Abou-el-makarim, J. Heully, J. Barthelat et al.,

, Effective Group Potentials. 2. Extraction and Transferability for Chemical Groups Involved in Covalent or Donor-Acceptor Bonds, J. Phys. Chem. A, vol.105, pp.206-214, 2001.

H. Stoll, G. Wagenblast, and H. Preuss, On the Use of Local Basis Sets for Localized Molecular Orbitals, Theor. Chim. Acta, vol.57, pp.169-178, 1980.

A. Fornili, M. Sironi, and M. Raimondi, Determination of Extremely Localized Molecular Orbitals and Their Application to Quantum Mechanics/Molecular Mechanics Methods and to the Study of Intramolecular Hydrogen Bonding, J. Mol. Struct. (THEOCHEM), vol.632, pp.157-172, 2003.

M. Sironi, A. Genoni, M. Civera, S. Pieraccini, and M. Ghitti, Extremely Localized Molecular Orbitals: Theory and Applications, Theor. Chem. Acc, vol.117, pp.685-698, 2007.
URL : https://hal.archives-ouvertes.fr/hal-02196453

X. Assfeld and J. Rivail, Quantum Chemical Computations on Parts of Large Molecules: the Ab Initio Local Self Consistent Field Method, Chem. Phys. Lett, vol.263, pp.100-106, 1996.

N. Ferré, A. Assfeld, and J. Rivail, Specific Force Field Parameters Determination for the Hybrid Ab Initio QM/MM LSCF Method, J. Comput. Chem, vol.23, pp.610-624, 2002.

P. Loos and X. Assfeld, Core-Ionized and Core-Exited States of Macromolecules, Int. J. Quantum Chem, vol.107, pp.2243-2252, 2007.

A. Monari, J. Rivail, and X. Assfeld, Advances in the Local Self Consistent Field Method for Mixed Quantum Mechanics/Molecular Mechanics Calculations, Acc. Chem. Res, vol.46, pp.596-603, 2013.
URL : https://hal.archives-ouvertes.fr/hal-02189224

M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb et al., , 2009.

J. F. Amacher, P. R. Cushing, C. D. Bahl, T. Beck, and D. R. Madden, Stereochemical Determinants of C-terminal specificity in PDZ Peptide-binding Domains, J. Biol. Chem, vol.288, pp.5114-5126, 2013.

S. F. Boys and F. Bernardi, Calculation of Small Molecular interactions by Differences of Separate Total Energies -Some Procedures with Reduced Errors, Mol. Phys, vol.19, pp.553-566, 1970.

T. A. Jones, J. Y. Zou, S. W. Cowan, and M. Kjeldgaard, Improved Methods for Building Protein Models in Electron Density Maps and the Location of Errors in these Models, Acta Crystallogr., Sect. A, vol.47, pp.110-119, 1991.

A. Genoni, L. Bu?inský, N. Claiser, J. Contreras-garcía, B. Dittrich et al., Quantum Crystallography: Current Developments and Future Perspectives, Chem. Eur. J, vol.24, pp.10881-10905, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01819260

R. F. Novara, A. Genoni, and S. Grabowsky, What is Quantum Crystallography? ChemViews, 2018.

S. Grabowsky, A. Genoni, and H. Bürgi, Quantum Crystallography, Chem. Sci, vol.8, pp.4159-4176, 2017.
URL : https://hal.archives-ouvertes.fr/hal-02196481

L. Massa and C. F. Matta, Quantum Crystallography: A Perspective, J. Comput. Chem, vol.39, pp.1021-1028, 2017.

V. Tsirelson, Early Days of Quantum Crystallography: A Personal Account, J. Comput. Chem, vol.39, pp.1029-1037, 2017.

S. C. Capelli, H. Bürgi, B. Dittrich, S. Grabowsky, and D. Jayatilaka, Hirshfeld Atom Refinement. IUCrJ, vol.1, pp.361-379, 2014.

M. Woi?ska, S. Grabowsky, P. M. Dominiak, K. Wo?niak, and D. Jayatilaka, Hydrogen atoms can be located accurately and precisely by x-ray crystallography, Sci. Adv, 2016.

G. Morra, A. Genoni, M. A. Neves, K. M. Merz, . Jr et al., Molecular Recognition and Drug-Lead identification: What Can Molecular Simulations Tell Us?

, Med. Chem, vol.17, pp.25-41, 2010.

L. Legnani, F. Compostella, F. Sansone, and L. Toma, Cone calix[4]arenes with orientable glycosylthioureido groups at the upper rim: an in-depth analysis of their symmetry properties, J. Org. Chem, vol.80, pp.7412-7418, 2015.

M. Ferraro, I. D'annessa, E. Moroni, G. Morra, A. Paladino et al., Allosteric Modulators of HSP90 and HSP70: Dynamics Meets Function through Structure-Bases Drug Design, J. Med. Chem, vol.62, pp.60-87, 2019.