A. Warshel and M. Levitt, Theoretical studies of enzymic reactions: Dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme, Journal of Molecular Biology, vol.103, issue.2, p.227, 1976.
DOI : 10.1016/0022-2836(76)90311-9

U. Singh and P. Kollman, A combinedab initio quantum mechanical and molecular mechanical method for carrying out simulations on complex molecular systems: Applications to the CH3Cl + Cl? exchange reaction and gas phase protonation of polyethers, Journal of Computational Chemistry, vol.107, issue.6, p.718, 1986.
DOI : 10.1016/B978-0-12-164720-9.50006-4

S. Antonczak, G. Monard, M. Ruiz-lopez, and J. Rivail, Modeling of Peptide Hydrolysis by Thermolysin. A Semiempirical and QM/MM Study, Journal of the American Chemical Society, vol.120, issue.34, p.8825, 1998.
DOI : 10.1021/ja981650u

M. Harrison, N. Burton, and I. Hillier, Catalytic Mechanism of the Enzyme Papain:?? Predictions with a Hybrid Quantum Mechanical/Molecular Mechanical Potential, Journal of the American Chemical Society, vol.119, issue.50, p.12285, 1997.
DOI : 10.1021/ja9711472

G. Monard, M. Loos, V. Thery, K. Baka, and J. Rivail, Hybrid classical quantum force field for modeling very large molecules, International Journal of Quantum Chemistry, vol.20, issue.2, p.153, 1996.
DOI : 10.1021/bi00514a028

T. Skarzynski, P. Moody, and A. Wonacott, Structure of holo-glyceraldehyde-3-phosphate dehydrogenase from Bacillus stearothermophilus at 1.8 ?? resolution, Journal of Molecular Biology, vol.193, issue.1, p.171, 1987.
DOI : 10.1016/0022-2836(87)90635-8

D. Brown, The gmq User Manual; available at www.lctn.u-nancy.fr/Chercheurs, 1998.

J. Stewart, Optimization of parameters for semiempirical methods I. Method, Journal of Computational Chemistry, vol.24, issue.2, p.209, 1989.
DOI : 10.1093/comjnl/6.2.163

E. Coitino, K. Irving, J. Rama, A. Iglesias, N. Paulino et al., Theoretical studies of hydrogen-bonded complexes using semiempirical methods, Journal of Molecular Structure: THEOCHEM, vol.210, p.405, 1990.
DOI : 10.1016/0166-1280(90)80065-V

E. Coitino, O. Ventura, and R. Sosa, Comparative ab initio and semi-empirical study of hydrogen bonded complexes of NH3 and H2O, Journal of Molecular Structure: THEOCHEM, vol.254, p.315, 1992.
DOI : 10.1016/0166-1280(92)80076-X

B. Kallies and R. Mitzner, The Ability of the Semiempirical PM3 Method to Model Proton Transfer Reactions in Symmetric Hydrogen Bonded Systems, Journal of Molecular Modeling, vol.1, issue.2, p.68, 1995.
DOI : 10.1007/s0089450010068

D. Rinaldi, P. Hoggan, C. Ab, D. Rinaldi, P. Hoggan et al., 584a, QCPE, p.128, 1989.

F. Talfournier, N. Colloc-'h, J. Mornon, and G. Branlant, Comparative study of the catalytic domain of phosphorylating glyceraldehyde-3-phosphate dehydrogenases from bacteria and archaea via essential cysteine probes and site-directed mutagenesis, European Journal of Biochemistry, vol.252, issue.3, p.447, 1998.
DOI : 10.1046/j.1432-1327.1998.2520447.x