Date of Award

January 2015

Degree Type


Degree Name

Doctor of Philosophy (PhD)


Medicinal Chemistry and Molecular Pharmacology

First Advisor

Markus Lill

Committee Member 1

Jean-Christophe Rochet

Committee Member 2

Chiwook Park

Committee Member 3

Daisuke Kihara


Quantitative Structure-Activity Relationship (QSAR) methods are a commonly used tool in the drug discovery process. These methods attempt to form a statistical model that relates descriptor properties of a ligand to the activity of that ligand compound towards a specific desired physiological response. QSAR methods are known as a ligand-based method, as they specifically use information from ligands and not protein structural data. However, a derivation of QSAR methods are pseudoreceptor methods. Pseudoreceptor methods go beyond standard QSAR by building a model representation of the protein pocket. However, the ability of pseudoreceptors to accurately replicate natural protein surfaces has not been studied. The goal of this thesis work is to investigate the necessary descriptors to map a protein binding pocket and a method to accurately recreate the 3-D spatial structure of the binding pocket. In addition, additional applications of existing pseudoreceptor methods are explored.