Reviews in Computational Chemistry Volume 18
Reviews in Computational Chemistry Volume 18
Reviews in Computational Chemistry Volume 18
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80 The Use of Scor<strong>in</strong>g Functions <strong>in</strong> Drug Discovery Applications<br />
69. A. N. Ja<strong>in</strong>, J. Comput.-Aided Mol. Design, 10, 427 (1996). Scor<strong>in</strong>g Non-Covalent Prote<strong>in</strong><br />
Ligand Interactions: A Cont<strong>in</strong>uous Differentiable Function Tuned to Compute B<strong>in</strong>d<strong>in</strong>g<br />
Aff<strong>in</strong>ities.<br />
70. W. Welch, J. Ruppert, and A. N. Ja<strong>in</strong>, Chem. Biol., 3, 449 (1996). Hammerhead: Fast, Fully<br />
Automated Dock<strong>in</strong>g of Flexible Ligands to Prote<strong>in</strong> B<strong>in</strong>d<strong>in</strong>g Sites.<br />
71. M. D. Elridge, C. W. Murray, T. R. Auton, G. V. Paol<strong>in</strong>i, and R. P. Mee, J. Comput.-Aided<br />
Mol. Design, 11, 425 (1997). Empirical Scor<strong>in</strong>g Functions. I. The Development of a Fast<br />
Empirical Scor<strong>in</strong>g Function to Estimate the B<strong>in</strong>d<strong>in</strong>g Aff<strong>in</strong>ity of Ligands <strong>in</strong> Receptor Complexes.<br />
72. C. W. Murray, T. R. Auton, and M. D. Elridge, J. Comput.-Aided Mol. Design, 12, 503<br />
(1999). Empirical Scor<strong>in</strong>g Functions. II. The Test<strong>in</strong>g of an Empirical Scor<strong>in</strong>g Function for the<br />
Prediction of Ligand-Receptor B<strong>in</strong>d<strong>in</strong>g Aff<strong>in</strong>ities and the Use of Bayesian Regression to<br />
Improve the Quality of the Method.<br />
73. H.-J. Boehm, J. Comput.-Aided Mol. Design, 12, 309 (1998). Prediction of B<strong>in</strong>d<strong>in</strong>g Constants<br />
of Prote<strong>in</strong> Ligands: A Fast Method for the Prioritization of Hits Obta<strong>in</strong>ed From De Novo<br />
Design or 3D Database Search Programs.<br />
74. Y. Takamatsu and A. Itai, Prote<strong>in</strong>s: Struct., Funct., Genet., 33, 62 (1998). A New Method for<br />
Predict<strong>in</strong>g B<strong>in</strong>d<strong>in</strong>g Free Energy Between Receptor and Ligand.<br />
75. R. Wang, L. Liu, L. Lai, and Y. Tang, J. Mol. Model., 4, 379 (1998). SCORE: A New<br />
Empirical Method for Estimat<strong>in</strong>g the B<strong>in</strong>d<strong>in</strong>g Aff<strong>in</strong>ity of a Prote<strong>in</strong>–Ligand Complex.<br />
76. D. Rognan, S. L. Lauemoller, A. Holm, S. Buus, and V. Tsch<strong>in</strong>ke, J. Med. Chem., 42, 4650<br />
(1999). Predict<strong>in</strong>g B<strong>in</strong>d<strong>in</strong>g Aff<strong>in</strong>ities of Prote<strong>in</strong> Ligands from Three-Dimensional Models:<br />
Application to Peptide B<strong>in</strong>d<strong>in</strong>g to Class I Major Histocompatibility Prote<strong>in</strong>s.<br />
77. C. Bissantz, G. Folkers, and D. Rognan, J. Med. Chem., 43, 4759 (2000). Prote<strong>in</strong>-Based<br />
Virtual Screen<strong>in</strong>g of Chemical Databases. 1. Evaluation of Different Dock<strong>in</strong>g/Scor<strong>in</strong>g<br />
Comb<strong>in</strong>ations.<br />
78. M. Stahl and M. Rarey, J. Med. Chem., 44, 1035 (2001). Detailed Analysis of Scor<strong>in</strong>g<br />
Functions for Virtual Screen<strong>in</strong>g.<br />
79. G. E. Kellogg, G. S. Joshi, and D. J. Abraham, Med. Chem. Res., 1, 444 (1991). New Tools for<br />
Model<strong>in</strong>g and Understand<strong>in</strong>g Hydrophobicity and Hydrophobic Interactions.<br />
80. E. C. Meng, I. D. Kuntz, D. J. Abraham, and G. E. Kellogg, J. Comput.-Aided Mol. Design, 8,<br />
299 (1994). Evaluat<strong>in</strong>g Docked Complexes With the HINT Exponential Function and<br />
Empirical Atomic Hydrophobicities.<br />
81. C. Zhang, G. Vasmatzis, J. L. Cornette, and C. DeLisi, J. Mol. Biol., 267, 707 (1997).<br />
Determ<strong>in</strong>ation of Atomic Solvation Energies from the Structure of Crystallized Prote<strong>in</strong>s.<br />
82. R. S. DeWitte and E. I. Shakhnovich, J. Am. Chem. Soc., 1<strong>18</strong>, 11733 (1996). SMoG: De Novo<br />
Design Method Based on Simple, Fast and Accurate Free Energy Estimates. 1. Methodology<br />
and Support<strong>in</strong>g Evidence.<br />
83. R. S. DeWitte, A. V. Ishchenko, and E. I. Shakhnovich, J. Am. Chem. Soc., 119, 4608 (1997).<br />
SMoG: De Novo Design Method Based on Simple, Fast, and Accurate Free Energy Estimates.<br />
2. Case Studies <strong>in</strong> Molecular Design.<br />
84. J. B. O. Mitchell, R. A. Laskowski, A. Alex, and J. M. Thornton, J. Comput. Chem., 20, 1165<br />
(1999). BLEEP—A Potential of Mean Force Describ<strong>in</strong>g Prote<strong>in</strong>–Ligand Interactions. I.<br />
Generat<strong>in</strong>g the Potential.<br />
85. J. B. O. Mitchell, R. A. Laskowski, A. Alex, M. J. Forster, and J. M. Thornton, J. Comput.<br />
Chem., 20, 1177 (1999). BLEEP—A Potential of Mean Force Describ<strong>in</strong>g Prote<strong>in</strong>–Ligand<br />
Interactions. II. Calculation of B<strong>in</strong>d<strong>in</strong>g Energies and Comparison With Experimental<br />
Data.<br />
86. I. Muegge and Y. C. Mart<strong>in</strong>, J. Med. Chem., 42, 791 (1999). A General and Fast Scor<strong>in</strong>g<br />
Function for Prote<strong>in</strong>–Ligand Interactions: A Simplified Potential Approach.<br />
87. I. Muegge, Y. C. Mart<strong>in</strong>, P. J. Hajduk, and S. W. Fesik, J. Med. Chem., 42, 2498 (1999).<br />
Evaluation of PMF Scor<strong>in</strong>g <strong>in</strong> Dock<strong>in</strong>g Weak Ligands to the FK506 B<strong>in</strong>d<strong>in</strong>g Prote<strong>in</strong>.