Free Energy Calculations in Rational Drug Design

<strong>1.</strong> Historical Overview and Future Challenges; J.A. McCammon. <strong>Section</strong> <strong>One: Theory.</strong> <strong>2.</strong> Free Energy Calculations: Methods for Estimating Ligand Binding Affinities; D.A. Pearlman. <strong>3.</strong> Molecular Mechanics Force Field Development and Applications; P.M. Todebush, J.P. Bowen. <strong>Section</strong> <strong>Two: Molecular Properties.</strong> <strong>4.</strong> Solvation Thermodynamics and the Treatment of Equilibrium and Nonequilibrium Solvation Effects by Models Based on Collective Solvent Coordinates; C.J. Cramer, D.G. Truhlar. <strong>5.</strong> Relative Solvation Free Energies Calculated Using Explicit Solvent; A. Agarwal, et al. <strong>6.</strong> Tautomerism and Ionisation Studies Using Free Energy Methods; G.A. Worth, P.M. King. <strong>Section Three:</strong> <strong>Ligand Binding.</strong> <strong>7.</strong> Free Energy Calculations on Enzyme-Inhibitor Complexes: Studies of Thermolysin and Rhizopus Pepsin; B.G. Rao. <strong>8.</strong> Free Energy Calculations on DNA: Ligand Complexes; S.B. Singh, P.A. Kollman. <strong>Section Four: Ligand Design and Analysis.</strong> <strong>9.</strong> The Linear Interaction Energy Method for Computation of Ligand Binding Affinities; J. Åqvist, J. Marelius. <strong>10.</strong> New Free Energy Based Methods for Ligand Binding from Detailed Structure-Function to Multiple-Ligand Screening; S. Banba, et al. <strong>11.</strong> Ligand Interaction Scanning Using Free Energy Calculations; M.D. Erion, M.R. Reddy. <strong>12.</strong> MM-PBSA Applied to Computer-Assisted Ligand Design; B. Kuhn, et al. <strong>13.</strong> Reaction Free Energy Profiles Using Free Energy Perturbation and Coordinate Coupling Methodologies: Analysis of the Dihydrofolate Reductase Catalytic Mechanism; U.C. Singh, et al. <strong>Section Five: Drug</strong> <strong>Design Case Studies.</strong> <strong>14.</strong> Fructose 1,6-Bisphosphatase: Use of Free Energy Calculations in the Design and Optimization of AMP Mimetics; M.R. Reddy, M.D. Erion. <strong>15.</strong> COX-2, SRC SH2 Domain, HIV Reverse Transcriptase, and Thrombin: Computational Approaches to Protein-Ligand Binding; W.L. Jorgensen, et al. <strong>16.</strong> HIV-1 Protease: Structure-Based Drug Design Using the Free Energy Perturbation Approach; M.R. Reddy, K. Appelt. <strong>17.</strong> Thymidylate Synthase: Free Energy Calculations for Estimating Inhibitor Binding Affinities; T.-S. Lee, P.A. Kollman. <strong>18.</strong> Dihydrofolate Reductase: Free Energy Calculations for the Design of Mechanism-Based Inhibitors; J.E. Gready, P.L. Cummins. <strong>19.</strong> Adenosine Deaminase: Calculation of Relative Hydration Free Energy Differences; M.D. Erion, M.R. Reddy. Index.