NOTE: References for AMBER, CHARMm, MM3 and OPLS parameters are given separately below

Bol, J. E., Buning, C., Comba, P., Reedijk, J. and Strohle, M. (1998) Molecular mechanics modeling of organic backbone of metal-free and coordinated ligands, J. Comp. Chem. 19, 512-523

Cannon, J. F. (1993), J. Comp. Chem. 14, 995-1005.

Comba, P., and Hambley, T. W. (1995) Molecular Modeling of Inorganic Compounds, VCH, Weinheim, Germany.

Hay, B. P. (1993) Methods for molecular mechanics modeling of coordination compounds, Coord. Chem. Rev. 126, 177-236.

Hay, B. P., Yang, L., Lii, J-H., and Allinger, N. L. (1998) An extended MM3(96) force field for complexes of the group 1A and 2A cations with ligands bearing conjugated ether donor groups, Theochem: J. Molecular Structure 428, 203-219,

Hopfinger, A. J. & R. A. Pearlstein (1994), J. Comp. Chem. 5, 486-499.

Leach, A. R. (1996) Molecular Modeling Principles and Applications, Addison Wesley, Longman Limited, Essex, England

Liang, G. Y., Fox, P. C., and Bowen, J. P. (1996) Parameter Analysis and refinement toolkit system and its application in MM3 parameterization for Phosphine and its derivatives, J. Comp. Chem. 17, 940-953.

Norrby, P-O., and Liljefors, T. (1998) Automated molecular mechanics parameterization with simultaneous utilization of experimental and quantum mechanical data, J. Comp. Chem. 19, 1146-1166.

Orozco, M., & Luque, F. J., (1993), J. Comp. Chem. 14, 881-894.

Palma, P. N. L. (1998), "Studies of Macromolecular Recognition and Prediction of Redox Properties of Metalloproteins," Doctoral Dissertation, Universidade Nova de Lisboa, Portugal.

Salahub, D. R., and Zerner, M. C. (1989) The Challenge of d and f electrons, American Chemical Society, Washington, D. C.

Wampler, J. E. (1994) Computational Chemistry and Molecular Modeling of Electron Transfer Proteins, IN Methods in Enzymology (Peck, H. D., Jr., LeGall, J., Eds) Academic Press, New York, pp. 559-607.

Jorgensen, W. L., & Tirado-Rives, J.,(1988) The OPLS Potential Functions for Proteins. Energy Minimization for Crystals of Cyclic Peptides and Crambin, J. Am. Chem. Soc. 110, 1657-1666.

Kaminski, G., Duffy, E. M. Matsui, T., and Jorgensen, W. L. (1994) J. Phys. Chem. 98, 13077-13082.

Lii, J-H., & Allinger, N. L. (1989a) Molecular Mechanics. The MM3 Force Field for Hydrocarbons. 2. Vibrational Frequencies and Thermodynamics, J. Am. Chem. Soc. 111, 8566-8575.

Lii, J-H., & Allinger, N. L. (1989b) Molecular Mechanics. The MM3 Force Field for Hydrocarbons. 3. The van der Waals Potentials and Crystal data for Aliphatic and Aromatic Hydrocarbons, J. Am. Chem. Soc. 111, 8576-8582.

Lii, J-H., & Allinger, N. L. (1991) The MM3 Force Field for Amides, Polypeptides and Proteins, J. Comp. Chem. 12, 186-199.

Lii, J-H., & Allinger, N. L. (1998) Directional Hydrogen Bonding in the MM3 Force Field. II. J. Comp. Chem. 19, 1001-1016.

Weiner, P. K., & Kollman, P. A., (1981) AMBER: Assisted Model Building with Energy Refinement. A General Program for Modeling Molecules and Their Interactions, J. Comp. Chem. 2, 287-303.

Weiner, S.J., Kollman, P.A., Case, D.A., Singh, U.C., Ghio, C., Alagona, G., Profeta, S., Jr., Weiner, P.K. (1984) A new force field for molecular mechanical simulation of nucleic acids and proteins. J. Am. Chem. Soc. 106, 765-784.

Weiner, S. J., Kollman, P. A., Nguyen, D. T., and Case, D. A., (1986) "An All Atom Force Field for Simulations of Proteins and Nucleic Acids," J. Comp. Chem. 7, 230-252.

Cornell, W. D., Cieplak, P., Bayly, C. I., Gould, I. R., Merz, K. M. Jr., Ferguson, D. M. Spellmeyer, D. C., Fox, T., Caldwell, J. W., and Kollman, P. A. (1995) A second generation force field for the simulation of proteins, nucleic acids and organic molecules, J. Am. Chem. Soc. 117, 5179-5197.

Brooks, B.R., Bruccoleri, R.E., Olafson, B.D., States, D.J., Swaminathan, S., Karplus, M. CHARMM: A program for macromolecular energy, minmimization, and dynamics calculations. J. Comp. Chem. (1983) 4, 187-217.

Momany, F. A., & Rone, R., (1992) Validation of the General Purpose QUANTA 3.2/CHARMm Force Field, J. Comp. Chem. 13, 888-900.