Free Energy Calculations in Rational Drug Design

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