Overview of Rational Drug Design, Conformational and Energetic Aspects of Receptor-Ligand Recognition, New Free Energy Calculation Methods for Structure-Based Drug Design and Prediction of Protein Stability, Binding Evaluation Using the Finite Difference Solution to the Linearized Poisson-Boltzmann Equation and salvation Entropy Correction, SmoG: A Ligand Design Method Based on Knowledge-Based Parametrization of a Solvent Reorganization Model, The Evaluation of Multi-Body Dynamics for Studying Ligand-Protein Interactions: Using MBO (N)D to Probe the Unbinding Pathways of Cbz-Val-Phe-Phe-Val-Cbz from the Active Site of HIV-1 Phase, Calculation of Relative Hydration Free Energy Differences for Heteroaromatic Compounds: Use in the Design of AMP Deaminase Inhibitors, New Tools for Rational Drug Design, Rational Approaches to Inhibition of Human Osteoclast Cathepsin K and Treatment of Osteoporosis, Building a Hypothesis for Nucleotide Transport Inhibitors Unified Pharmacophoric Model for Cannabinoids and Aminoalkylindoles Derived from Molecular Superimposition of CB Cannabinoid Receptor Agonists CP55244 and WIN55212-2.