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Reviews in Computational Chemistry Volume 18

Reviews in Computational Chemistry Volume 18

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References 79<br />

51. M. A. Hossa<strong>in</strong> and H.-J. Schneider, Chem. Eur. J., 5, 1284 (1999). Flexibility, Association<br />

Constants, and Salt Effects <strong>in</strong> Organic Ion Pairs: How S<strong>in</strong>gle Bonds Affect Molecular<br />

Recognition.<br />

52. K. P. Murphy, D. Xie, K. S. Thompson, L. M. Amzel, and E. Freire, Prote<strong>in</strong>s: Struct., Funct.,<br />

Genet., <strong>18</strong>, 63 (1994). Entropy <strong>in</strong> Biological B<strong>in</strong>d<strong>in</strong>g Processes: Estimation of Translational<br />

Entropy Loss.<br />

53. J. Hermans and L. Wang, J. Am. Chem. Soc., 119, 2702 (1997). Inclusion of Loss of<br />

Translational and Rotational Freedom <strong>in</strong> Theoretical Estimates of Free Energies of B<strong>in</strong>d<strong>in</strong>g.<br />

Application to a Complex of Benzene and Mutant T4 Lysozyme.<br />

54. R. S. Bohacek and C. McMart<strong>in</strong>, J. Med. Chem., 35, 1671 (1992). Def<strong>in</strong>ition and Display of<br />

Steric, Hydrophobic, and Hydrogen-Bond<strong>in</strong>g Properties of Ligand B<strong>in</strong>d<strong>in</strong>g Sites <strong>in</strong> Prote<strong>in</strong>s<br />

Us<strong>in</strong>g Lee and Richards Accessible Surface: Validation of a High-Resolution Graphical Tool<br />

for Drug Design.<br />

55. D. H. Williams, M. S. Searle, J. P. Mackay, U. Gerhard, and R. A. Maplestone, Proc. Natl.<br />

Acad. Sci. U.S.A., 90, 1172 (1993). Toward an Estimation of B<strong>in</strong>d<strong>in</strong>g Constants <strong>in</strong> Aqueous<br />

Solution: Studies of Associations of Vancomyc<strong>in</strong> Group Antibiotics.<br />

56. H.-J. Boehm, J. Comput.-Aided Mol. Design, 8, 243 (1994). The Development of a Simple<br />

Empirical Scor<strong>in</strong>g Function to Estimate the B<strong>in</strong>d<strong>in</strong>g Constant for a Prote<strong>in</strong>–Ligand Complex<br />

of Known Three-Dimensional Structure.<br />

57. H.-J. Boehm, D. W. Banner, and L. Weber, J. Comput.-Aided Mol. Design, 13, 51 (1999).<br />

Comb<strong>in</strong>atorial Dock<strong>in</strong>g and Comb<strong>in</strong>atorial <strong>Chemistry</strong>: Design of Potent Non-Peptide<br />

Thromb<strong>in</strong> Inhibitors.<br />

58. S.-S. So and M. Karplus, J. Comput.-Aided Mol. Design, 13, 243 (1999). A Comparative<br />

Study of Ligand–Receptor Complex B<strong>in</strong>d<strong>in</strong>g Aff<strong>in</strong>ity Prediction Methods Based on Glycogen<br />

Phosphorylase Inhibitors.<br />

59. M. D. Miller, S. K. Kearsley, D. J. Underwood, and R. P. Sheridan, J. Comput.-Aided Mol.<br />

Design, 8, 153 (1994). FLOG: A System to Select ‘‘Quasi-Flexible’’ Ligands Complementary<br />

to a Receptor of Known Three-Dimensional Structure.<br />

60. G. Jones, P. Willett, and R. C. Glen, J. Mol. Biol., 245, 43 (1995). Molecular Recognition of<br />

Receptor Sites Us<strong>in</strong>g a Genetic Algorithm With a Description of Desolvation.<br />

61. G. Jones, P. Willett, R. C. Glen, A. R. Leach, and R. Taylor, J. Mol. Biol., 267, 727 (1997).<br />

Development and Validation of a Genetic Algorithm for Flexible Dock<strong>in</strong>g.<br />

62. D. K. Gehlhaar, G. M. Verkhivker, P. A. Rejto, C. J. Sherman, D. B. Fogel, L. J. Fogel,<br />

and S. T. Freer, Chem. Biol., 2, 317 (1995). Molecular Recognition of the Inhibitor AG-<br />

1343 by HIV-1 Protease: Conformationally Flexible Dock<strong>in</strong>g by Evolutionary Programm<strong>in</strong>g.<br />

63. G. M. Verkhivker, D. Bouzida, D. K. Gehlhaar, P. A. Reijto, S. Arthurs, A. B. Colson, S. T.<br />

Freer, V. Larson, B. A. Luty, T. Marrone, and P. W. Rose, J. Comput.-Aided Mol. Design,<br />

14, 731 (2000). Decipher<strong>in</strong>g Common Failures <strong>in</strong> Molecular Dock<strong>in</strong>g of Ligand–Prote<strong>in</strong><br />

Complexes.<br />

64. M. Rarey, B. Kramer, T. Lengauer, and G. Klebe, J. Mol. Biol., 261, 470 (1996). A Fast<br />

Flexible Dock<strong>in</strong>g Method Us<strong>in</strong>g an Incremental Construction Algorithm.<br />

65. M. Rarey, B. Kramer, and T. Lengauer, J. Comput.-Aided Mol. Design, 11, 369 (1997).<br />

Multiple Automatic Base Selection: Prote<strong>in</strong>–Ligand Dock<strong>in</strong>g Based on Incremental Construction<br />

Without Manual Intervention.<br />

66. M. Rarey, S. Wef<strong>in</strong>g, and T. Lengauer, J. Comput.-Aided Mol. Design, 10, 41 (1996).<br />

Placement of Medium-Sized Molecular Fragments <strong>in</strong>to Active Sites of Prote<strong>in</strong>s.<br />

67. M. Rarey, B. Kramer, and T. Lengauer, Bio<strong>in</strong>formatics, 15, 243 (1999). Dock<strong>in</strong>g of Hydrophobic<br />

Ligands With Interaction-Based Match<strong>in</strong>g Algorithms.<br />

68. R. D. Head, M. L. Smythe, T. I. Oprea, C. L. Waller, S. M. Green, and G. R. Marshall, J. Am.<br />

Chem. Soc., 1<strong>18</strong>, 3959 (1996). VALIDATE: A New Method for the Receptor-Based<br />

Prediction of B<strong>in</strong>d<strong>in</strong>g Aff<strong>in</strong>ities of Novel Ligands.

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