In the absence of three-dimensional (3D) structures of potential drug targets, ligand-based drug design is one of the popular approaches for drug discovery and lead optimization. 3D quantitative structure-activity relationships (3D QSAR) and pharmacophore modeling are the most important and widely used tools in ligand-based drug design that can provide crucial insight of the nature of the interactions between drug target and ligand molecule and provide predictive models suitable for lead compound optimization. The work presented in this thesis will discuss the features and potential application of recent advances in ligand-based drug design, along with a detailed description of a novel 3D QSAR method based on the conformationally sample pharmacophore (CSP) approach (denoted CSP-SAR).