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Some Biological Applications of Semiempirical MO Theory

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3D QSAR in Drug Design

Part of the book series: Three-Dimensional Quantitative Structure Activity Relationships ((QSAR,volume 2))

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References

  1. Ferenczy, G.G., Rivail, J-L., Surján P.R. and Náray-Szab!o, G., NDDO fragment self-consistent field approximation for large electronic systems, J. Comput. Chem., I3 (1992) 830–837.

    Google Scholar 

  2. Náray-Szab!o, G., Towards a molecular orbital method for the conformational analysis of very large biomolecules. Acta Phys. Acad. Sci. Hung., 40 (1976) 261–273.

    Google Scholar 

  3. Stewart. J.J.P., Application of localized molecular orbitals to the solution of semiempirical selfconsistent field equations. Int. J. Quant. Chem., 58(1996) 133–146.

    Article  CAS  Google Scholar 

  4. Zhao, Q. and Yang, W., Analytical energy gradients and geometry optimisation in the divide-and-conquer methods for large molecules, J. Chem. Phy., 102 (1995) 9598–9603.

    CAS  Google Scholar 

  5. Yang, W. and Lee, T.-S., A density-matrix divide-and-conquer approach for electronic sturcture calculations of large molecules, J. Chem. Phps., 103 (1995) 5674–5678.

    CAS  Google Scholar 

  6. Lee. T.-S., York, D. M. and Yang, W., Linear scaling semiempirical quantum calculations of macromolecules, J. Chem. Phys., 105 (1996) 274–42750.

    Google Scholar 

  7. Dixon, S.L. and Merz, Jr. K.M., Semiempirical molecular orbital calculations with linear system size scaling, J. Chem. Phys., 104 (1996) 6643–6649.

    CAS  Google Scholar 

  8. White, C.A., Johnson. B G., Gill, P.M.W. and Head-Gordon. M., The continuous fast multiple method, 230 (1994) 8–18.

    CAS  Google Scholar 

  9. Strain, M.C., Scuseria, G.E. and Frisch. M.J., Achieving linear scaling for the electronic Coulomb problem, Science 271 (1996) 51–53

    CAS  Google Scholar 

  10. Teeter, M.M., Roe. S.M. and Heo, N.H., Atomic resolution (0.83 Angstr/om) crystal structure of the hydrophobic protein crambin at 130 K, J. Mol. Biol., 230 (1993) 292–311.

    Article  CAS  Google Scholar 

  11. Deisenhofer., J., Crystallographic refinement of the structure of bovine pancreatic typsin inhibitor at 1.5 Å resolution, Acta Crystallograph. B, 31 (1975) 238–250.

    Google Scholar 

  12. Stewart. J.J.P., MOPAC7 Version 2 manual, QCPE. Bloomington, IN. 1993.

    Google Scholar 

  13. Klamt, A. and Schürmann, G., COSMO: A new approach to dielectric screening in solvents with explicit expressions for the screening energy and its gardients, Perkin Trans., 2 (1993) 799–805.

    Google Scholar 

  14. Troung, T.N. and Stephanovich, E.V., Analytical first and second energy derivatives of the generalized conductorlike screening model for free energy of solvation, J. Chem. Phys., 103 (1995) 3709–3717.

    Google Scholar 

  15. Andzelm, J., Kölnmel, C. and Klamt, A., Incorporation of solvent effects into density functional calculations of molecular energies and geometries, J. Chem. Phys., 103 (1995) 9312–9320.

    Article  CAS  Google Scholar 

  16. York, D., Lee, T.S. and Yang, W., Chem. Phys. Lett. (submitted).

    Google Scholar 

  17. Washel, A. and Levitt, M., Thoeretical studies of enzymic reactions: 1. Dielectric electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme, J. Mol. Biol., 103 (1976) 227–235.

    Google Scholar 

  18. Field. M.J., Bash, P.A. and Karplus, M., A combined quantum mecahnical and molecular mechanical potential for molecular dynamics simulation, J. Comput. Chem., 11 (1990) 700–733.

    Article  CAS  Google Scholar 

  19. Vasiyev, V.V., Bliznyuk, A.A and Voityuk, A.A., A combined quantum chemical molecular mechanical study of hydrogen bonded systems, Int. J. Quant. Chem., 44 (1992) 897–930.

    Google Scholar 

  20. Théory, V., Rinaldi, D., Rivail, J.-L., Maigret, B. and Ferenczy. G.J., Quantum mechanical computations on very large systems: The local self-consistent self method, J. Comput. Chem., 15 (1994) 269–282

    Google Scholar 

  21. Thompson, M.A., Glendening E.D. and Feller. D., The nature of K+/crown ether interactions A hybrid quantum mecahnical-molecular mechanical study, J. Phys. Chem., 98 (1994) 10465–10476.

    Article  CAS  Google Scholar 

  22. Thompson, M.A., and Schenter, G.K., Excited states of the bacteriochlorophyll 6 dimer of rhodopseudomonas viridis: A QM/MM study of the photosynthetic reaction center that includes MM polarisation, J. Phs. Chem., 99 (1995) 6374–6386.

    CAS  Google Scholar 

  23. Bakowies, D. and Thiel, W., Hybrid models for combined quantum mechanical and molecular mechanical approcaches J. Phys. Chem., 100 (1996) 10580–10594.

    Article  CAS  Google Scholar 

  24. Alex, A., Beck, B., Lanig, H., Rauhut, G. and Clark, T. (paper in preparation)

    Google Scholar 

  25. Stanton. R.V., Hartsough, D.S. and Merz, Jr. K.M., An examination of a density functional/molecular mechanical coupled potential. J. Comput. Chem., 16 (1996) 113–128.

    Google Scholar 

  26. Bernardi, F., Olivucci, M. and Robb, M.A., Simulation of MC-SCF results on covalent organic multi-bonds reactions: Molecular mechanics with valence bond (MM-VB) J. Am. Chem. Soc., 114 (1992) 1606–1616.

    CAS  Google Scholar 

  27. Aqvist, J. and Warshel, A., Simulation of enzyme reactions using valence bond force fields and other hybrid quantum classical approaches, Chem. Rev., 93 (1993) 2523–2530.

    Google Scholar 

  28. Singh, U.C. and Kollman, P.A., A combined ab initio quantum mechanical and molecular mechanical method for carrying out simulations on complex molecular systems: Applications to the CH3C1 + C1 exchange reaction and gas phase protonation of polyethers, J. Comput. Chem., 7 (1986) 718–730.

    Article  CAS  Google Scholar 

  29. Allinger, N. L., Yuh, Y.H. and Lii, J.-H., MoIecular mechanics: The MM3 force field for hydrocarbons I. J.Am. Chem. Soc., 111 (1989) 8551–8582.

    CAS  Google Scholar 

  30. Pearlman, D.A, Case, D.A., Ross, J.W., Cheatham. III. T.E., Ferguson, D.M., Seibel, G.L., Singh, U.C., Weiner, P.K. and Kollman, P.A., AMBER 4.1, University of California, San Francisco, CA, 1995.

    Google Scholar 

  31. Brooks, B.R., Burccoleri, R.E., Olafson, B.D., States, D.J., Swaminathan, S. and Karplus, M., CHARMm: A program for macromolecular energy, minimization and dynamics calculations. J. Comput. Chem., 4 (1983) 187–217.

    Article  CAS  Google Scholar 

  32. Bash. P.A., Field, M.J. and Karplus, M., Free energy perturbation mehtod for chemical reactions in the condensed phase: A dynamical approach based on a Combined quantum and molecular mechanics potential J. Am. Chem. Soc., 109 (1987) 8092–8094.

    Article  CAS  Google Scholar 

  33. Gao, J., Absolute free energy of solution from Monte Cui-lo simulations using combined quantum and molecular mechanicalpotentials, J. Phys. Chem., 96 (1992) 537–540.

    CAS  Google Scholar 

  34. Gao, J. and Xia, X., A priori evaluation of aqueous polarization effects through Monte Carlo QM/MM simulations, Science, 258 (1992) 631–635.

    CAS  Google Scholar 

  35. Gao, J. and Pavelites, J.J., Aqueous basicity of the carboxvlate lone pairs and the C-O burrier in acetic acids: A combined quantum and statistical mechancal study, J. Am. Chem. Soc., 114 (1992) 1912–1914.

    CAS  Google Scholar 

  36. Gao, J., Hybrid quantum and molecular mechanical simulations: An alternative avenue to solvent effects in organic chemistry, Acc. Chem. Rea., 27 (1993) 298–305.

    Google Scholar 

  37. Gao, J., Luque, F.J. and Orozco, M., induced dipole moments and atomic charges based on average electrostatic potentials in aqueous solution, J. Chem. Phys., 98 (1993) 2975–2982.

    CAS  Google Scholar 

  38. Gao, J., Potential of mean force for the isomerization of DMF in aqueous solution: A Monte Carlo QM/MM simulation study J. Am. Chem. Soc., 115 (1993) 2930–2935.

    CAS  Google Scholar 

  39. Gao, J. and Xia, X., A tow-dimensional energy surface for a type II SN2 reaction in aqueous solution, J. Am. Chem. Soc., 115 (1993) 9667–9675.

    CAS  Google Scholar 

  40. Stanton, R.V., Hartsough. D.S. and Merz, Jr., K.M., Calculation of solvation free energies using a density funational molecular dynamics coupled potential, J. Phys. Chem., 97 (1993) 11868–11870.

    CAS  Google Scholar 

  41. Gao, J., Combined QM/MM simulation study of the Claisen rearrangement of allyl vinyl ether in aqueous solution, J. Am. Chem. Soc., 116 (1994) 1563–1564.

    CAS  Google Scholar 

  42. Liu, H. and Shi, Y., Combined molecular mechanical arid quantum mechanical potential study of a nucleophilic addition reaction in solution, J. Comput. Chem., 15 (1994) 1311–1318.

    CAS  Google Scholar 

  43. Liu, H., Müller-Plathe, F. and Van Gunsteren. W.F., A molecular dynamics simulation study with a combined quantum mechanical and molecualr mechanical potential energy function: Solvation effects on the conformational equilibrium of demethoxy ethane, J. Chem. Phys., 102 (1995) 1722–1730.

    CAS  Google Scholar 

  44. Hartsough, D.S. and Merz, Jr., K.M., Potential of mean force calculations on the SN1fragmentation of tert-butyl chloride, J.Phys. Chem., 99 (1995) 384–390.

    CAS  Google Scholar 

  45. Stanton, R.V., Little. L.R. and Merz, Jr., K.M., Quantum free energy perturbation study within a PM3/MM coupledpotential, J. Phys. Chem., 99 (1995) 483–486.

    CAS  Google Scholar 

  46. Thompson. M.A., Hybrid quantum mechanical/molecular mechanical force field development for large flexible molecules: A molecular dynamics study of 18-crown-6, J. Phys. Chem., 99 (1995) 4794–4804.

    CAS  Google Scholar 

  47. Bash. P.A., Field. M.J., Davenport. R.C., Petsko. G.A., Ringe. D. and Kaiplus. M., Structure of the triosephosphate isomerase phosphoglycolohydroxamate complex: An analog of the intermediate on the reaction pathway, Biochemistry 30 (1991) 5821–5826.

    Article  Google Scholar 

  48. Waszkowyez B., Hiller, I.H., Gensmantel. N. and Payling, D.W., Combined quantum mechanical-molecular mechanical study of catalysi is by the enzyme phospholipase A2: An investigation of the potential-energy surface for amide hydrolysis. J. Chem. Soc., Perkin Trans. 2 (1991) 225–2032.

    Google Scholar 

  49. Vasilyev, VV., Tetrahedral intermediate formation in the acylation step of acetylcholinesterases A combined quantum chemical and molecular mechanical model, J. Mol. Struct. (THEOCHEM), 304 (1994) 129–141.

    Article  Google Scholar 

  50. Elcock, A.H., Lyne, P.D., Mulholland, A J., Nandra. A. and Richards, W.G., Combined quantum and molecular mechanical study of DNA cross-linking by nitrous acid, J. Am. Chem. Soc., 117 (1995) 4706–4707.

    CAS  Google Scholar 

  51. Hartsough, D.S. and Merz, Jr., K.M., Dynamic force field models: Molecular dynamics simulations of human carbonic anhydrase II using a quantum mechanical/molecular mechanical coupled potential, J. Phy. Chem., 99 (1995) 11266–11275.

    CAS  Google Scholar 

  52. Born, M. and Von Karman, T., Über Schwingungen in Raumgittern, Physik. Z., 13 (1912) 297–309.

    CAS  Google Scholar 

  53. Brooks, III, C.L. and Kaiplus. M., Deformable stochastic boundaries in molecular dynamics J. Chem. Phys. 79 (1983) 6312–6325.

    CAS  Google Scholar 

  54. Brünger. A.T., Huber, R. and Kaiplus. M, Trysinogen-trypsin transition: A molecular dynamics study of induced conformational change in the activation domain, Biochemistry. 26 (1987) 5153–5164.

    Google Scholar 

  55. Davis, T.D., Maggiora, G.M. and Christoffersen. R.E., Ab initio calculations on large molecules using molecular fragments: Unrestricted Hartree fock calculations on low lying states of formaldehyde and its radical ions, J. Am. Chem. Soc., 96 (1974) 7878–7887.

    CAS  Google Scholar 

  56. Clementi, E.. Computational aspects for large chemical systems: Lecture notes in chemistry, Springer, New York, 1980.

    Google Scholar 

  57. Mascras, F. arid Morokunia, K., IMOMM: Anew integrated ab initio + molecular mechanics geometry optimisation scheme of equilibrium structures and transition states, J. Comput. Chem., 16 (1995) 1170–1179.

    Google Scholar 

  58. Bakowies, D. and Thiel, W., Semiempirical treatment of electrostatic potentials and partial charges in combined quantum mechanical, molecular mechanical approaches J. Comput. Chem., 17 (1996) 87–108.

    Article  CAS  Google Scholar 

  59. Thole, B.T., Molecular polarizabilities calculated with a modified dipole interaction. Chem. Phys., 59 (1981) 341–350.

    Article  CAS  Google Scholar 

  60. Monard, G., Loos M., Théry. V., Baka, K. and Rivail, J.-L., Hybrid classical quantum force field for modeling very large molecules, Int. J. Quant. Chem. 58 (1996) 153–159.

    Article  CAS  Google Scholar 

  61. Rappé, A.K., Caswit, C.J., Colwell, K.S., Goddard. III, W.A. and Skiff. W.M, UFF, a full periodic table force field for molecular mechanics and molecular dynamics simulations, J. Am. Chem. Soc., 114 (1992) 10024–10035.

    Google Scholar 

  62. Luzhkov, V. and Warshel, A., Microscopic calculations of solvent effects on absorption spectra of conjugated molecules, J. Am. Chem. Soc., 113 (1991) 4491–4499.

    Article  CAS  Google Scholar 

  63. Luzhkov, V. and Warshel, A., Microscopic models for quantum mechanical calculations of chemical processes in solution: LD/AMPAC and SCAAS/AMPAC calculations of solvation energies, J. Comput. Chem., 13 (1992) 199–213

    Article  CAS  Google Scholar 

  64. Vesely, F.J., N-particle dynamics of polarizable Stockmayer-type molecules, J.Comput. Phys., 24 (1977) 361–371.

    Article  CAS  Google Scholar 

  65. Ahlstrom, P., WallQvist, A., Engstrom. S. and Jonsson, B., A molecular dynamics study of polarizable water, Mol. Phys., 68 (1989) 563–581.

    Google Scholar 

  66. Dang, L.X., Rice. J.E., Caldwell, J. and Kollman, P.A., Ionsolvationin polarizablewater: Molecular dynamics simulation, J. Am. Chem. Soc., 113 (1991) 2481–2486.

    Article  CAS  Google Scholar 

  67. Thompson. M.A., QM/MMpol: A consistent model for solute/solvent polarization: Application to the aqueous solvation and spectroscopy of formaldehyd. acetaldehyd and acetone, J. Phys. Chem., 100 (1996) 14492–14507.

    CAS  Google Scholar 

  68. Gasteiger. J. and Marsili, M., Iterative partial equalization of orbital tronegativity: A rapid access to atomic charges, Tetrahedron. 36 (1990) 3219–3288.

    Google Scholar 

  69. Abraham, R.J. and Hudson, B., Charge calculations inmolecular mechanics III: Amino acids and peptides, J. Coinput. Chem., 6 (1985) 173–181. (b)._Abraham, R.J. and Smith, P.E., Charge calculations in molecular mechanics IV: A general method for conjugated systems, J. Comput. Chem., 9 (1987) 288–297.

    CAS  Google Scholar 

  70. Coulson, C.A. and Longuel-Higgins, H.C., The electrostatic structure of conjugated systems: 1. General theory, Proc. Roy. Soc., A191 (1947) 39–60.

    CAS  Google Scholar 

  71. Mulliken, R.S., Electronic population analysis on LCAO-MO molecular wave funations, I. J. Chem. Phys., 23 (1955) 1833–1840.

    CAS  Google Scholar 

  72. Williams, D.E., Net atomic charges and multipole models for the ab initio molecular electric potential, In Lipkowitz, K.B. and Boyd, D.B. (Eds.) Reviewsincomputational chemistry. Vol. 2. VCH, Weinheim, 1991,pp. 219–271.

    Google Scholar 

  73. Storer, J.W., Giesen, D.J., Cramer, C J. and Truhlar, D.G., Class IV cargemodels: A new semiempirical approach in quantum chemistry, J. Comput.-AidedMol. Design 9 (1995) 87–110.

    CAS  Google Scholar 

  74. Rappé, A.K. and Goddard, III. W.A., Charge egualibration for molecular dynamics simulation, J. Phys. Chem., 95 (1991) 3358–3363.

    Google Scholar 

  75. Chirlian, L.E. and Francl, M.M., Aomic charges derived from electrostatic potentials: A detailed study, J. Comput. Chem., 8 (1987) 894–905.

    Article  CAS  Google Scholar 

  76. Breneman, C.M, and Wiberg, K.B., Determining atom-centred monopoles from molecular electrostatic potentials: The need for high sampling density in formamide conformational analysis, J. Comput. Chem., 11 (1990) 361–373.

    Article  CAS  Google Scholar 

  77. Besler, B.H., Merz, Jr., K.M. and Kollman. P.A., Atomic charges derived from semiempirical methods, J. Comp. Chem., 11(1990) 431–439

    CAS  Google Scholar 

  78. Spackman, M.A., potential derived chargesusing a grodesic point selection scheme, J. Comput. Chem., 17 (1996) 1–18.

    Article  CAS  Google Scholar 

  79. Ferenczy, G.G., Reynolds, C.A. and Richards. W.G., Semiempirical AMI electrostatic potentials and AM1 electrostatic potential derived charges: A comparison with ab initio values, J. Coinput. Chem., 11(1990)159–169.

    CAS  Google Scholar 

  80. Orozco, M. and Luque, F.J., On the Use of AMI and MNDO wave functions to compute accurate electrostatic charges, J. Comput. Chem., 11 (1990)909–923.

    Article  CAS  Google Scholar 

  81. Beck, B., Glen, R.C. and Clark. T., VESPA: A new, fast approach to electrostatic potential-derived atomic charges from semiempirical methods, J. Comput. Chem., 18 (1907) 744–756.

    Google Scholar 

  82. Beck. B., Glen, R.C. and Clark, T., A detailedstudy of VESPA electrostatic potential-derivedatomic charges, J. Mol. Model., 1 (1995) 176–187.

    Article  CAS  Google Scholar 

  83. Heiden, W., Goetze, T. and Brickmann, J.. Fast generation of molecular surfaces from 3D data fields with echanced ‘marching cube’ algorithm, J. Comput. Chem., 14 (1993) 246–250.

    Article  CAS  Google Scholar 

  84. Marsili, M., Computation of volumes and surface areas of organic compounds, In Jochum, C., Hicks. M.G. and Sunkel, J. (Eds.) Physical property prediction in organic chemistr, Springer Verlag, Berlin, 1988, pp. 249–251.

    Google Scholar 

  85. Rauhut, G. and Clark, T., Multicenter point charge model for high-quolity molecular electrostatic potentials from AM1 calculations, J. Comput. Chem., 14 (1993) 503–509.

    Article  CAS  Google Scholar 

  86. Beck. B., Rauhut, G. and Clark. T., The naturalatomic orbitalpoint charge model for PM3: multipole moments and molecular electrostatic potentials, J. Comput. Chem., 15 (1 994) 1064–1073.

    Google Scholar 

  87. Bayly, C.I., Cieplak, P., Cornell. W.D. and Kollman. P.A., A wel-behaved electrostatic potential based method using restraints for deriving atomic charges: The RESP method, J. Phs. Chem., 97 (1993) 10269–10280.

    CAS  Google Scholar 

  88. Francl, M.M., Carey. C., Chirlian, L.E. and Gange, D.M., Charge fitto elestrostatic potentials: II. Can atomic charges unambiguously fit to electrostatic potentials, J. Comput. Chem., 17 (1996) 367–383.

    Article  CAS  Google Scholar 

  89. Stone, A.J., Distributed multipole analysis or how to describe a molecular charge distribution, Chem. Phys. Lett., 83 (1981)233–239.

    Google Scholar 

  90. Chipot, C., Ángyán, J., Ferenczy, G.G. and Scheraga, H.A., Transferable net atomic charges from a distributed multipole analysis for the description of electrostatic properties: A case study of staturated hydrocarbons, J. Phys. Chem., 97 (1993) 6628–6636.

    CAS  Google Scholar 

  91. Sokalski, W.A. and Sawaryn, A., Correlated molecular and cumulative atomic multipole omoments, J. Chem. Phys., 87 (1987) 526–534.

    Article  CAS  Google Scholar 

  92. Stogryn, D.E. and Strogryn. A.P., Molecular multipole moments, Mol.Phys., 11 (1966) 371–393.

    CAS  Google Scholar 

  93. Stewart, J.J.P., MOPAC: A semiempirical molecular orbital program, J. Comput.-Aided Mol. Design. 4 (1990) 11–12.

    Article  Google Scholar 

  94. Buckingham, A.D., Molecular quadrupole moments. Quart. Rev., I3 (1959) 183–214.

    Google Scholar 

  95. Perutz, M.F., Electrostatic effects in proteins, Science, 201 (1978) 1187–1191.

    CAS  Google Scholar 

  96. Warwicker. J. and Watson, H.C., Calculation of the electric potential in the active site cleft due to a-helix dipoles, J. Mol. Biol., 157 (1982) 671–679.

    Article  CAS  Google Scholar 

  97. Warshel, A. and Russel, S.T., Calculations of electrostatic interactions in biochemical systems in solution, Q. Rev. Biophys., 17 (1984) 283–291.

    CAS  Google Scholar 

  98. Giessner-Prettre, C. and Pullman. A., Molecular elec trostatic potentials: Comparison of ab initio and CNDO results, Theor. Chim. Acta, 25 (1972) 83–89

    Article  CAS  Google Scholar 

  99. Alhambra, C., Luque, F.J. and Orozco, M., Comparison of NDDO and quasi-ab initio approoches to compute semiempiricalmolecular electrostatic potentials. J. Coinput. Chem., 15 (1994) 12–22.

    CAS  Google Scholar 

  100. Luque, F.J., Illas, F. and Orozco, M., Comparative study of the molecular elertrosatic potenrial obtained from different wavefunctions: Reliability of the semiempirical MNDO wavefunction, J. Comput. Chem., 11 (1990) 416–430.

    Article  CAS  Google Scholar 

  101. Luque, F.J. and Orozco, M., Reliability ofthe AMI wavefunction to compute molecular electrostatic potentials, Chem. Phys. Lett., 168 (1990) 269–275.

    Article  CAS  Google Scholar 

  102. Alemán, C., Luque, F.J. and Orozco, M, Suitability of the PM3-derived molecular electrostatic potentials, J. Comput. Chem., 14 (1993) 799–808.

    Google Scholar 

  103. Bharadwaj, R., Windemuth, A., Sridharan, S., Honig. B. and Nicholls, A., The fastmultipole boundary element method for molecular electrostatics: An optimal approach for large systems, J. Comput. Chem., 16 (1995) 898–913.

    Article  CAS  Google Scholar 

  104. Gaussian 92. Frisch, M.J., Trucks. G.W., Head-Gordon. M., Gill, P.M.W., Wong, M.W., Foresman, J.B., Johnson, B.G., Schlegel, H.B., Robb, M.A., Replogle. E.S., Gomperts, R., Andres, J.L., Raghavachari, K., Binkley. J.S., Gonzales, C., Martin. R.L., Fox, D.J., Defrees, D.J.C., Baker. J., Stewart, J.J.P. and Pople, J.A., Gausian lnc., Pittsburgh. PA. 1992.

    Google Scholar 

  105. Ford, G.P. and Wang, B., New approach to the rapid semiempirical calculation of molecular electrostatic potentialsbasedon the AMI wave function: Comparison wiih ab initio HF6-31G# results, J.Comput. Chem., 14(1993) 1101–1111.

    Article  CAS  Google Scholar 

  106. Nakajima, H., Takahashi, O. and Kikuchi. O., Rapid evaluation of molecular electrostaticpotential maps for aminoacids, peptides and proteins by empirical functions, J. Comput. Chem., 17 (1996) 790–805.

    Article  CAS  Google Scholar 

  107. Lyne, P.D., Mulholland, A.J. and Richards. W.G., Insights into chorismate mutase catalysisfrom a combined QM/MM simulation of the enzyme reaction, J. Am. Chem. Soc., 117 (1995) 11345–11350.

    Article  CAS  Google Scholar 

  108. Mulholland, A.J. and Karplus, M., Simulations of enzymic reactions, Biochem. Soc. Trans. 24 (1996) 247–254.

    CAS  Google Scholar 

  109. Beck. B., Lanig, H., Glen. R.C. and Clark. T., J. Med. Chem. (submitted).

    Google Scholar 

  110. Alex, A. and Finn, P., Fourth World Congress of Theoretically Oriented Chemists-WATOC’96, Jerusalem. Israel, 1996.

    Google Scholar 

  111. Lanig, H., Beck, B. and Clark. T., Poster, MGMS Meeting, York,U.K, 1996.

    Google Scholar 

  112. Jones, G., Willet, P. and Glen. R.C., Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation, J. Mol. Biol., 245 (1995) 43–53.

    CAS  Google Scholar 

  113. Rauhut, G., Alex. A., Chandrasekhar, J., Steinke, T., Sauer, W., Beck. R., Hutter, M., Gedeck, P. and Clark, T., VAMP6.0, OxfordMolecularLtd., Medawar Centre. Oxford Science Park, Sandford-on-Thames, Oxford OX4 4GA, U.K.

    Google Scholar 

  114. Weber. I.T., Steitz. T.A., Bubis. J. and Taylor. S.S., Predicted structures (cAMP binding domains of type 1 and type II regulatory subunits of CAMP-dependent protein kinase, Biochemistry. 26 (1987) 343–351.

    CAS  Google Scholar 

  115. McKay, D.B. and Steitz. T.A., Structure ofcatabolite gene activator protein at 2.9 Åresolution suggests binding to left handed B-DNA, Nature, 290 (1981) 744–749.

    Article  CAS  Google Scholar 

  116. Weber. I.T., and Steitz. T.A., Structure of a complex between catabolite gene activator protein and cyclic AMP refined at 2.5 Åresolution, J. Mol. Biol., 198 (1987) 311–326.

    Article  CAS  Google Scholar 

  117. Stehle, T. and Schulz, G.E., Three-dimensional structure of the complex bemeen guanylate kinase from yeast with its substrate GMP, J. Mol. Biol., 211 (1990) 249–254.

    Article  CAS  Google Scholar 

  118. Stehle, T. and Schulz, G.E., Refined structure of the complex between guanylare kinase and its substrate GMP, J.Mol. Biol., 224 (1992) 1127–1141.

    Article  CAS  Google Scholar 

  119. Mangani, S., Carloni, P. and Orioli, P., Crystal structure of the complex between carboxypeptidase A and the biproduct analog inhibitor L-benzylsuccinate at 2.0 Åresolution, J. Mol. Biol., 223 (1992) 573–578.

    Article  CAS  Google Scholar 

  120. Cappalonga, A.M., Alexander, R.S. and Christianson, D.W., Structural comparison of sulfodiimine in-hibitors in their complexes with zinc enzymes, J. Mol. Biol., 267 (1992) 19192–19197.

    CAS  Google Scholar 

  121. Kim, H. and Lipscomb. W.N., Comparison of the structures of three carboxypeptidase A-phosphonate complexes determined by X-ray crystallography, Biochemistry, 30 (1991) 8171–8180.

    CAS  Google Scholar 

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Beck, B., Clark, T. (2002). Some Biological Applications of Semiempirical MO Theory. In: Kubinyi, H., Folkers, G., Martin, Y.C. (eds) 3D QSAR in Drug Design. Three-Dimensional Quantitative Structure Activity Relationships, vol 2. Springer, Dordrecht. https://doi.org/10.1007/0-306-46857-3_8

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  • DOI: https://doi.org/10.1007/0-306-46857-3_8

  • Publisher Name: Springer, Dordrecht

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