1) Allen, M.P., Tildesley: Computer Simulations of Liquids, Clarendon, Oxford, 1987

5.0References

1) Allen, M.P., Tildesley: Computer Simulations of Liquids, Clarendon, Oxford, 1987.

2) Allinger, N.L., and Schleyer, P.V., J. Comp. Chem. (1996), 17, pp 385.

3) Bartnicki-Gracia, S., Annu. Rev. Microbiol., (1968), 22, pp 87.

4) Berendsen, H.J.C., Postma, J.P.M., van Gunsteren, W. F., and Hermans, J. in B.Pullman (Ed.): Intermolecular Forces, Reidel, Dordrecht , 1981, pp 331.

5) Berendsen H.J.C., and van Gunsteren, W.F., in Molecular dynamics simulation of statistical mechanical systems. Proceedings of the Enrico Fermi Summer School, Varenna 1985 pp 43-65.

6) Berendsen, H.J.C., Grigera, J.R., Straatsma, T.P., J. Phys. Chem. (1987), 91, pp 6269.

7) Bernstein, B.E., Michels, P.A.M.,. Hol, W.G.J., Nature, (1997), 385, pp 275.

8) Blake, C.F., Nature, (1997), 385, pp 204.

9) Brameld, K.A., Dasgupta, S. , and Goddard III, W.A., J. Phys. Chem., (1997), B101, pp 4851.

10) Brameld, K.A., and Goddard III, W.A., J. Am. Chem. Soc. (1998), 120, pp 3571.

11) Brameld, K.A., and Goddard III, W.A., Proc. Natl. Acad. Sci. (1998), 95, pp 4276.

12) Brooks, B.R. , Bruccoleri, R.E., Olafson, B.D., States, D. J., Swaminathan, and M. Karplus, J.Comput. Chem. (1983), 4 , pp 187.

13) Che, J., Cagin, T., and Goddard III, W. A., J. Phys. Chem. (1999) accepted.

14) Chen, Z.M., Cagin, T., and Goddard III, W.A., J. Comp. Chem. (1997), 18, pp 1365.

15) Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. A. J. Am. Chem. Soc.1995, 117, 5179-5197.

16) Collinge , D.B., Kragh, K.M., Mikkelsen, J.D., Nielsen, K.K., Rasmussen, U., Vad, K., Plant J. (1993), 3, pp 31.

17) Couch, R.B., in Virology, eds. Fields, B.N., and Knipe, D.M., (1990), Raven, New York. pp 607.

18) Cunningham, M.A., and Bash, P.A., Biochimie, (1997), 79, pp 687.

19) Dasgupta, S., Yamasaki, T., and Goddard III, W.A., J. Chem. Phys. , (1996), 104, 2898.

20) Debe, D., Carlson, M.J., and Goddard III, W.A., Proc. Natl. Acad. Sci. USA (1999), 96 , pp 2596.

21) Demiralp, E., Cagin, T., Huff, N.T., and Goddard III, W.A., XVIII Intl. Congress on Glass Proc., M. K. Choudhary, N. T. Huff, and C. H. Drummond III Editors, pp 11 (1998).

22) Demiralp, E., Cagin, T., and Goddard III, W.A., Phys.l Rev. Lett. (1999), 82, pp 1708.

23) Ding, H.Q., Karasawa, N., and Goddard III, W.A., J. Chem. Phys. (1992), 97, pp4309.

24) Fujita, T. (1990) in Comprehensive Medicinal Chemistry (Hansch, C. ED), pp-497-560, Pergamon, Oxford;

25) de Leeuw, S.W., Perram, J.W. , Smith, E.R. , Proc. Roy.Soc. London (1980) A373, 27.

26) Ewald, P., Ann. Phys. (Leipzig) (1921), 64, pp 253.

27) Fanelli, F. Menziani, C., Scheer, A., Cotecchia, S., and De Benedetti, P.D., Methods, (1998), 14, pp 302-317.

28) Figuerido, F., Levy, R.M., Zhou, R.H., and Berne , B.J., J. Chem. Phys. (1997), 107, pp 7002.

29) Floriano, W.B., Nascimento, M.A.C., Domont, G.B., and Goddard III, W.A., Proteins: Structure, Function and Genetics, (1998), accepted.

30) Franke , A.R., (1984) Theoretical Drug Design Methods, Elsevier, Amsterdam;

31) Fukamizo, T., Kramer, K.J., Insect. Biochem., (1985), 15, pp 141.

32) Gerdy, J. .J., Ph.D thesis , "Accurate Interatomic Potentials for Simulations", 1995, California Institute of Technology.

33) Hagler, A. T., Huler, E., and Lifson, S. J. Am. Chem. Soc. (1974), 96, 5319.

34) Hart, P.J., Pfluger, H.D., Monzingo, A.F., Hollis, T., Robertus, J.D., J. Mol. Biol. (1995), 248, pp 402.

35) Henrissat, B., Bairoch, A., Biochem. J. (1993), 293, pp 781.

36) Hermans, J., Berendsen, H.J.C., van Gunsteren, W.F., and Postma, J.P.M., Biopolymers, (1984), 23, 1513.

37) Heyes, D.M. , J. Chem. Phys. (1981), 74, pp 1924.

38) Hodes, Z. I. , Nemethy, G., and Scheraga, H. A. , Biopolymers, (1979),18, pp 1565.

39) Jain, A., Vaidehi, N., and Rodriguez, G., J. Comp. Phys., (1993), 106, pp258.

40) Jorgensen, W.L. , Chandrasekar, J. , Madura, J.D., Impey, R.W., Klein. M. L., J. Chem. Phys. (1983), 79, pp 962.

41) Jorgensen, W. L. Tirado-Tives, J. J. Am. Chem. Soc. (1988), 110, pp 1657.

42) Karasawa, N., Goddard III, W.A. , J. Phys. Chem., (1989), 93, pp 7320.

43) Kier, L.B., and Testa, B., (1995), in Advances in drug research , Testa , B., and Meyer U.A., Eds. Vol 26, pp1-43 Academic Press, London).

44) Koga, D., Isogai, A., Sakuda, S., Matsumoto, S., Suzuki, A., Kimura , S., Ide, A., Agri. Biol. Chem. (1987), 51, pp 471.

45) Kramer, K.J., Dziadik- Turner, C., Koga, D., in Comprehensive Insect Physiology, Biochemistry and Pharmacology: Integument, Respiration and Circulation, (1985), Pergamon Press, Oxford.

46) Kuranda , M.J., Robbins, P.W., J. Biol. Chem. (1991), 266, pp 19758.

47) Levitt, M. J. Mol. Biol. (1983), 168, pp 595.

48) Levitt, M., Hirshberg, M., Sharon-R., Laidig, K.E., and Dagett, V., J. Phys. Chem. (1997), B101, pp 5051.

49) Lim, K.T., Brunett, S., Iotov, M., McClurg, B., Vaidehi, N., Dasgupta, S. Taylor, S., and Goddard III, W.A., J. Comp. Chem. (1997), 18, pp 501.

50) Mackerell, A.D., Wiorkiewicz-Kuczera, J., Karplus, M., J. Am. Chem. Soc. (1995), 117, pp 11946-11975.

51) Marrone, T.J., Straatsma, T.P., Briggs, J.M., Wilson D.K., Quiocho, F.A., and McCammon, J.A., J. Med.Chem., 1996, 39, pp 277.

52) Marrone, T.J., zbriggs, J.M., and McCammon, J.A., Ann. Rev. Pharmacol. Toxicol., 1997, 37, pp 71.

53) Mathiowetz, A., Jain, A., Karasawa, N., and W.A. Goddard III, Proteins: Structure,Function and Genetics, (1994), 20, 2273.

54) Mayo, S. L.; Olafson, B. D.; Goddard, W. A. J. Phys. Chem.1990, 94, 8897-8909.

55) Mazur, A. Abagayan, R.J., Biomol. Struct. Dyn. (1989), 6, pp 815.

56) McCammon, J.A., in Dynamics of Proteins and Nucleic Acids, (1987), Cambridge.

57) McPhillips, T.M., Hsu, B.T., Sherman, M.A., Mas, M.T., and Rees, D.C., Biochem. (1996), 35, pp 4118.

58) Miklis, P., Cagin, T., and Goddard III, W.A., J. Am. Chem. Soc. (1997), 119, 7458.

59) Mommany, F. A., McGuire, R.F., Burgess, A. W. , Scheraga, H.A. , J. Phys. Chem. (1975), 79, 2361.

60) Montorsi, M., Menziani, M.C., Cocchi, M., Fanelli, F., and De Benedetti, P.G., Methods, (1998), 145, pp239-254.

61) Monzingo, A.F., Marcotte, E.M., Hart, P.J,., Robertus, J.D., Nat. Struct. Biol. (1996), 3, pp 133.

62) Nose, S., Mol Phys. (1984), 52, pp 255.

63) Parr, R.G.and Yang,W. in Density Functional Theory of Atoms and Molecules, (1989), Clarendon Press, Oxford(England).

64) Parinello, M., and Rahman, A., J. Appl. Phys. (1981), 52, pp 7182.

65) Perrakis, A., Tews, I., Dauter Z., Oppenheim, A.B., Chet, I., Wilson, K.S., Vorgais, C.E., Structure, (1994), 2, pp 1169.

66) Plaxco, K.W., and Goddard III, W.A., Biochem, (1994), 33, 3050.

67) Pople, J.A., and Beveridge D.L. in Approximate Molecular Orbital Theory”, Mc Graw-Hill, New York, 1970.

68) Pranata, J., Wierschke, S.G., Jorgensen, W.L., J. Am. Chem. Soc., (1991), 113, pp 2810.

69) Qi, Y., Cagin, T., Kimura, Y., and Goddard III, W.A., Phys. Rev. B (1999), 59, pp 3527.

70) Rahman, A. and Stillinger, F.H., J. Chem. Phys. ,(1971), 55, pp 3336.

71) Rappe, A.K., and Goddard III, W.A., J. Chem. Phys., (1991), 95, pp 3358.

72) Rappé, A. K.; Casewit, C. J.; Colwell, K. S.; Goddard, W. A., III; Skiff, W. M. J. Am. Chem. Soc.1992, 114, 10024-10035.

73) Rice, L.M., Brunger, A.T., Proteins: Structure, Function and Genetics, (1994), 19, pp 277.

74) Ringnalda, M. N.; Langlois, J.-M.; Greeley, B. H.; Murphy, R. B.; Russo, T. V.; Cortis, C.; Muller, R. P.; Marten, B.; Donnelly, R. E.; Mainz, D. T.; Wright, J. R.; Pollard, W. T.; Cao, Y.; Won, Y.; Miller, G. H.; Goddard, W. A., III; Friesner, R. A. Jaguar 3.0 from Schrödinger, Inc. located in Portland, OR.

75) Rueckert, R.R., in Fundamental Virology, (1991), eds, Fields, B.N., and Knipe, D.M., Raven, New York.

76) Ryckaert, J.P., Cicotti, G., and Berendsen, H.J.C., J. Comp. Phys (1977), 23, 327. Hoover, W.G., Phys. Rev., (1985), A31, 1695.

77) Sadanobu,J., and Goddard III, W.A., J. Chem. Phys., (1997), 106, pp 6722.

78) Schaefer, H.F. in Quantum Chemistry: the development of Ab initio methods inmolecular electronic structure theory, (1984), Oxford(England), Clarendon Press.

79) Sternberg, M. J. E. , Protein Structure Prediction, Oxford Univ. Press, 1996.

80) Tannor, D.J., Marten, B., Murphy, R., Friesner, R.A., Sitkoff, D., Nicholls, A., Ringnalda, M., Goddard III, W.A., Honig, B., J. Am. Chem. Soc. (1994), 116, pp 11875.

81) Vaidehi, N., Jain, A. and Goddard III, W.A., J. Phys. Chem., (1996), 100, pp 10508.

82) Vaidehi, N., and Goddard III, W.A., Proc. Natl Acad. Sci. USA, (1997), 94, pp 2466.

83) Vaidehi, N., McPhillips, T.M., and Goddard III, W.A., 1998, in preparation.

84) van Gunsteren, W.F., Berendsen, H.J.C.:Groningen Molecular Simulation (GROMOS) Library Manual, Biomos, Groningen, 1987.

85) van Gunsteren, W.F., and Weiner, P.K., in Computer Simulation of Biomolecular Systems; (1989), Leiden .

86) van Gunsteren, W.F., and Berendsen H.J.C., Ang. Chem. Int. Ed. Engl. (1990), 29, pp 992.

87) Warshel, A., in Computer Modeling of Chemical Reactions in Enzymes and Solutions, (1991), Wiley.

88) Watanabe , T., Suzuki, K., Oyanagi, W., Ohnishi, K., Tanaka, H., J. Biol. Chem. (1990), 265, pp 15659.

89) Weiner , S.J., Kollman, P.A., Case, D.A., Singh, U.C., Ghio, C., Alagona, G., Profeta, S., Weiner , P.J., J. Am. Chem. Soc. (1984), 106, pp 765.

90) Weiner, S. J. , Kollman, P.A. ,Nguyen, D. T., and Case, D.A. , J. Comput. Chem. (1986), 7, pp 230.

91) Woodcock, L.V., Chem. Phys. Lett., (1971), 10, pp 257.

92) Zwanzig, R.W., J. Chem. Phys. (1956), 22, pp 1420.

1