Author's School

Graduate School of Arts & Sciences

Author's Department/Program

Biology and Biomedical Sciences: Computational and Systems Biology


English (en)

Date of Award

January 2009

Degree Type


Degree Name

Doctor of Philosophy (PhD)

Chair and Committee

Garland Marshall


This dissertation discusses two main projects from my thesis work. The first project focuses on the development of a small molecule docking program, SKATE, for drug discovery. The second project focuses on the critical analysis of the thermal stability of a mini-protein, FSD-1. SKATE is a novel approach to small molecule docking. It removes any inter-dependence between sampling and scoring to improve docking accuracy. SKATE systematically and exhaustively samples a ligand's conformational, rotational and translational degrees of freedom, as constrained by a receptor pocket, to find sterically allowed poses. A total of 266 ligands were re-docked to their respective receptors to assess SKATE's performance. The results show that SKATE was able to sample poses within 2 Angstrom RMSD of the native structure for 97% of the cases. The best performing scoring function was able to rank a pose that is within 2 Angstrom RMSD of the native structure as the top-scoring pose for 83% of the cases. Compared to published data, SKATE has a higher self-docking accuracy rate than or is at least comparable to GOLD, Glide, MolDock and Surflex. The cross-docking accuracy of SKATE was assessed by docking 83 ligands to their respective receptors. The cross-docking results were comparable to those in published methods. Mini-proteins that contain fewer than 50 amino acids often serve as model systems for studying protein folding because their small size makes long time-scale simulations possible. However, not all mini-proteins are created equal. The stability and structure of FSD-1, a 28-residue mini-protein that adopts the Beta Beta Alpha zinc-finger motif independent of zinc binding, was investigated using circular dichroism: CD), differential scanning calorimetry: DSC), and replica-exchange molecular dynamics: REMD). FSD-1's broad melting transition, similar to that of a helix-to-coil transition, was observed in CD, DSC, and REMD experiments. The N-terminal -hairpin was found to be flexible. FSD-1's apparent melting temperature of 41 degrees C may be a reflection of the melting of its alpha-helical segment instead of the entire protein. Thus, FSD-1's status as a model system for studying protein folding should be reconsidered despite its attractiveness for being small in size and it was designed to contain essential helix, sheet, and turn secondary structures. An electronic copy of this dissertation is available online at


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