Protein folding has long been viewed as being rich in complexities. With the development of the energy landscape theory, our view of protein folding, however, has greatly simplified from the hopelessly complex one first presented by Levinthal’s paradox. Because of their funneled energy landscapes, global structural measures of similarity to the native state are clearly adequate for describing the folding progression for most natural proteins. Quantifying the energetic and entropic competition, which is pivotal to any folding reaction, is still sometimes not sufficient. We are interested in studying fundamental questions of the mechanisms of protein folding and to formulate the forces that bias an efficient folding. While most efforts in folding research have focused in recent year on small proteins, exploring the folding of larger proteins is of high interest. Additionally, studying anomalous folding phenomena may serve to understand the rule. As an example, we may mention the remarkably diverse folding kinetics of some structurally homologous proteins. Finally, often proteins undergo posttranslational modifications that are important to regulate their function. We study the effects of these modifications on the protein thermodynamics and kinetics.