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Progress in force-field calculations of molecular interaction fields and intermolecular interactions

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Perspectives in Drug Discovery and Design

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References

  1. Burkert, U. and Allinger, N.L., Molecular mechanics, ACS Monograph 177, American Chemical Society, Washington D.C., 1982.

    Google Scholar 

  2. Siebel, G.L. and Kollman, P.A., Molecular mechanics and the Modeling of drug structures, In Comprehensive medicinal chemistry, Vol. 4, Hansch C., Sammes P.G., Taylor, J.B. and Ramsden, C.A. (Eds.), Pergamon Press, Oxford, 1990, pp. 125–138.

    Google Scholar 

  3. Goodford, P., The properties of force fields, In Sanz, F., Giraldo, J. and Manaut, F. (Eds.) QSAR and molecular modeling: Concepts, computational tools and biological applications, Prous Science Publishers, Barcelona, 1995, pp. 199–205.

    Google Scholar 

  4. Hehre, W.J., Radom, L., v.R. Schleyer, P. and Pople, J.A., Ab initio molecular orbital theory, John Wiley & Sons, New York, 1986.

    Google Scholar 

  5. Gundertofte, K., Liljefors, T., Norrby, P.-O. and Pettersson, I., A comparison of conformational energies calculated by several molecular mechanics methods, J. Comput. Chem., 17 (1996) 429–449. (b) Pettersson, I. and Liljefors, T., Molecular mechanics calculated conformational energies of organic molecules, In Lipkowitz, K.B. and Boyd, D.B. (Eds.) Reviews in Computational Chemistry, Vol. 9, VCH Publishers, Inc., New York, 1996, pp. 167–189.

    Google Scholar 

  6. Cramer, III, R.D., Patterson, D.E. and Bunce, J.D., Comparative molecular field analysis (CoMFA): 1. Effect of shape on binding of steriods to carrier proteins, J. Am. Chem. Soc., 110 (1988) 5959–5967.

    Google Scholar 

  7. Goodford, P.J., A computational procedure for determining energetically favorable binding sites on biologically important macromolecules, J. Med. Chem., 28 (1985) 849–857.

    Google Scholar 

  8. Boobbyer, D.N.A., Goodford, P.J., McWhinnie, P.M. and Wade, R.C., New hydrogen-bond potentials for use in determining energetically favourable binding sites on molecules of known structure, J. Med. Chem., 32 (1989) 1083–1094.

    Google Scholar 

  9. Wade, R.C., Clark, K. and Goodford, P.J., Further development of hydrogen-bond functions for use in determining energetically favorable binding sites on molecules of known structure: 1. Ligand probe groups with the ability to form two hydrogen bonds, J. Med. Chem., 36 (1993) 140–147.

    Google Scholar 

  10. Wade, R.C., Clark, K. and Goodford, P.J., Further development of hydrogen-bond functions for use in determining energetically favorable binding sites on molecules of known structure: 2. Ligand probe groups with the ability to form more than two hydrogen bonds, J. Med. Chem., 36 (1993) 148–156.

    Google Scholar 

  11. Goodford, P., Multivariate characterization of molecules for QSAR analysis, J. Chemometrics, 10 (1996) 107–111.

    Google Scholar 

  12. Cramer, III, R.D., DePriest, S.A., Patterson, D.E. and Hecht, P., The developing practice of comparative molecular field analysis, In Kubinyi, H. (Ed.) 3D QSAR in drug design: Theory, methods and applications, ESCOM Science Publishers, Leiden, 1993, pp. 443–485.

    Google Scholar 

  13. Folkers, G., Merz, A. and Rognan, D., CoMFA: Scope and limitations, In Kubinyi, H. (Ed.) 3D QSAR in drug design: Theory, methods and applications, ESCOM Science Publishers, Leiden, 1993, pp. 583–618.

    Google Scholar 

  14. Kroemer, R.T. and Hecht, P. Replacement of steric 6–12 potential-derived interaction energies by atom-based indicator variables in CoMFA leads to models of higher consistency, J. Comput.-Aided Mol. Design, 9 (1995) 205–212.

    Google Scholar 

  15. Floersheim, P., Nozulak, J. and Weber, H.P., Experience with comparative molecular fields analysis, In Wermuth, C.G. (Ed.) Trends in QSAR and molecular modelling 92 (Proceedings of the 9th European Symposium on Structure-Activity Relationships: QSAR and Molecular Modeling), ESCOM Science Publishers, Leiden, 1993, pp. 227–232.

    Google Scholar 

  16. Berendsen, H.J.C., Electrostatic interactions, In van Gunsteren, W.F., Weiner, P.K. and Wilkinson, A.J. (Eds.) Computer simulation of biomolecular systems: Theoretical and experimental applications, Vol. 2, ESCOM Science Publishers, Leiden, 1993, pp. 161–181.

    Google Scholar 

  17. Kim, K. H. and Martin, Y.C. Direct prediction of linear free energy substituent effects from 3D structures using comparative molecular field analysis: 1. Electronic effects of substituted benzoic acids, J. Org. Chem., 34 (1991) 2723–2729.

    Google Scholar 

  18. Gasteiger, J. and Marsili, M., Iterative partial equalization of orbital electronegativity: A rapid access to atomic charges, Tetrahedron, 36 (1980) 3219–3228.

    Google Scholar 

  19. Chirlian, L.E. and Francl, M.M., Atomic charges derived from electrostatic potentials: A detailed study, J. Comput. Chem., (1987) 894–905. (b) Besler, B.H., Merz, Jr., K.M. and Kollman, P.A., Atomic charges derived from semiempirical methods, J. Comput. Chem., 11 (1990) 431–439

    Google Scholar 

  20. Kroemer, R.T., Hecht, P. and Liedl, K.R., Different electrostatic descriptors in comparative molecular field analysis: A comparison of molecular electrostatic and coulomb potentials, J. Comput. Chem., 11 (1996) 1296–1308.

    Google Scholar 

  21. Wade, R.C., Molecular interaction fields, In Kubinyi, H. (Ed.) 3D QSAR in drug design, Theory, methods and applications, ESCOM Science Publishers, Leiden, 1993, pp. 486–505.

    Google Scholar 

  22. Goodford, P., GRID user guide, Edition 15, Molecular Discovery Ltd., Oxford, UK, 1997.

    Google Scholar 

  23. Liljefors, T. and Norrby, P.-O., unpublished results.

  24. Mills, J.E.J. and Dean, P.M., Three-dimensional hydrogen-bond geometry and probablity information from a crystal survey, J. Comput.-Aided Mol. Design, 10 (1996) 607–622.

    Google Scholar 

  25. Clementi, S., Cruciani G., Riganelli, D. and Valigi, R., GOLPE: Merits and drawbacks in 3D-QSAR, In Sanz, F., Giraldo, J. and Manaut, F. (Eds.) QSAR and molecular modelling: Concepts, computational tools and biological applications, Prous Science Publishers, Barcelona, 1996, pp. 408–414.

    Google Scholar 

  26. Goodford, P., personal communication.

  27. Bemis, G.W. and Murcko, M.A., The properties of known drugs: 1. Molecular frameworks, J. Med. Chem., 39 (1996) 2887–2983.

    Google Scholar 

  28. Dougherty, D.A., Cation-interactions in chemistry and biology: A new view of benzene, Phe, Tyr, and Trp, Science, 271 (1996) 163–168.

    Google Scholar 

  29. Dougherty, D.A., and Stauffer, D.A., Acetycholine binding by a synthetic receptor: Implications for biological recognition, Science, 250 (1990) 1558–1560.

    Google Scholar 

  30. Sussman, J.L., Harel, M., Frolow. F., Oefner, C., Goldman, A., Toker, L. and Silman, I., Atomic structure of acetylcholinesterase from Torpedo californica: A prototypic acetycholine-binding protein, Science, 253 (1991) 872–879. (b) Harel, M., Quinn, D.M., Nair, H. K., Silman, I. and Sussman, J.L., The X-ray structure of a transi-tion state analog complex reveals the molecular origin of the catalytic power and substrate specificity of acetylcholinesterase, J. Am. Chem. Soc., 118 (1996) 2340–2346.

    Google Scholar 

  31. Caldwell, J.W. and Kollman, P.A., Cation-interactions: Nonadditive effects are critical in their accurate representation, J. Am. Chem. Soc., 117 (1995) 4177–4178.

    Google Scholar 

  32. Kim, K.S., Lee, J.Y., Lee, S.J., Ha, T.-K. and Kim, D.H., On binding forces between aromatic ring and quaternary ammonium compound, J. Am. Chem. Soc., 116 (1994) 7399–7400.

    Google Scholar 

  33. Caldwell, J., Dang, L.X. and Kollman, P.A., Implementation of nonadditive intermolecular potentials by use of molecular dynamics: Development of a water-water potential and water-ion cluster interactions, J. Am. Chem. Soc., 112 (1990) 9144–9147.

    Google Scholar 

  34. Meng, E.C., Cieplak, P., Caldwell, J.W. and Kollman, P.A., Accurate solvation free energies of acetate and methylammonium ions calculated with a polarizable water model J. Am. Chem. Soc., 119 (1994) 12061–12062.

    Google Scholar 

  35. Mecozzi, S., West, Jr., A.P. and Dougherty, D.A., Cation-interactions in simple aromatics: Electrostatics provide a predictive tool, J. Am. Chem. Soc., 118 (1996) 2307–2308.

    Google Scholar 

  36. Cheney, B.V., Schultz, M.W., Cheney, J. and Richards, W.G., Hydrogen-bonded complexes involving benzene as an H-acceptor, J. Am. Chem. Soc. 110 (1988) 4295–4198.

    Google Scholar 

  37. Rodham, D.A., Suzuki, S., Suenram, R.D., Lovas, F.J., Dasgupta, S., Goddard, III, W.A. and Blake, G.A., Hydrogen bonding in the benzene-ammonia dimer, Nature, 363 (1993) 735–737.

    Google Scholar 

  38. Trumpp-Kallmeyer, S., Hoflack, J., Bruinvels, A. and Hibert, M., Modeling of G-protein-coupled receptors: Application to dopamine, adrenaline, serotonin, acetylcholine, and mammalian opsin receptors, J. Med. Chem., 35 (1992) 3448–62.

    Google Scholar 

  39. Liljefors, T. and Norrby, P.-O., Ab initio quantum chemical model calculations on the interactions between monoamine neurotransmitters and their receptors, In Schwartz, T.W., Hjort, S.A. and Sandholm Kastrup, J. (Eds.) Structure and function of 7TM receptors, Alfred Benzon Symposium 39, Munksgaard, Copenhagen, 1996, pp. 194–207.

  40. Liljefors, T. and Norrby, P.-O., An ab initio study of the trimethylamine-formic acid and the trimethy-lammonium- formate anion complexes, their monohydrates and continuum solvation, J. Am. Chem. Soc., 119 (1997) 1052–1058.

    Google Scholar 

  41. Williams, D.E., Coulombic interaction in crystalline hydrocarbons, Acta Cryst., A30 (1974) 71–77.

    Google Scholar 

  42. Pettersson, I. and Liljefors, T., Benzene-benzene (phenyl-phenyl) interactions in MM2/MMP2 molecular mechanics calculations, J. Comput. Chem., 8 (1987) 139–145.

    Google Scholar 

  43. Burley, S.K. and Petsko, G.A., Aromatic-aromatic interaction: A mechanism of protein structure stabilization, Science, 229 (1985) 23–28.

    Google Scholar 

  44. Burley, S.K. and Petsko, G.A., Dimerization energetics of benzene and aromatic amino acid side chains, J. Am. Chem. Soc., 108 (1986) 7995–8001.

    Google Scholar 

  45. Singh, J. and Thornton, J.M., The interaction between phenylalanine rings in proteins, FEBS Lett., 191 (1985) 1–6.

    Google Scholar 

  46. Chipot, C., Jaffe, R., Maigret, B., Pearlman, D.A. and Kollman, P.A., Benzene dimer: A good model for ≠-≠ interactions in proteins? A comparison between the benzene and the toluene dimers in the gas phase and in aqueous solution, J. Am. Chem. Soc., 118 (1996) 11217–11224.

    Google Scholar 

  47. Schauer, M. and Bernstein, E.R., Calculations of the geometry and binding energy of aromatic dimers: benzene, toluene, and toluene-benzene, J. Chem. Phys., 82 (1985) 3722–3727.

    Google Scholar 

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Liljefors, T. Progress in force-field calculations of molecular interaction fields and intermolecular interactions. Perspectives in Drug Discovery and Design 9, 3–17 (1998). https://doi.org/10.1023/A:1027224402069

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