Physical Modeling of Protein Folding

Sequence-based models for protein folding are developed and tested on peptides with both alpha- and beta-structure, and on small three-helix-bundle proteins. The interaction potentials of the models are minimalistic and based mainly on hydrogen bonding and effective hydrophobicity forces. By contrast, the geometric representation of the protein chain is detailed. We explore the thermodynamic behaviors of these models by using efficient Monte Carlo methods, and focus on obtaining a realistic physical description of the folding process. In particular, we investigate dynamical aspects of folding, such as `two-state' behavior and secondary structure formation. In addition, the thesis includes a study on similarity measures for protein structures.