The history of the protein folding problem dates back 35 years to the publication of the first software tool for protein structure prediction. As can be expected, significant progress has been made since these early days. One way to track this progress is to follow the Critical Assessment of Protein Structure Prediction (CASP) initiative, which studies methods and techniques oriented towards protein structure prediction on a global scale, focusing on emerging technologies, modern computing resources and novel infrastructures. The aim of this book is to approach the presented problem not from a predictive standpoint, but rather by introducing a model which attempts to simulate - as far as possible - the folding process as it takes place in vivo. The book is broad in scope - starting with ab initio models and attempting to construct a mechanistic model on the basis of their predictions. This model, if sufficiently reliable, may influence the interpretation of biological processes related to protein folding. The authors' computational model is expected to go beyond experimental studies, casting a new light on the complexities of biological phenomena. It acknowledges the geometric properties of the polypeptide chains as well as the influence of external force fields (particularly the aqueous environment in which the folding process takes place) and external molecules, including specific ligands. Elements of information theory applied to the folding process seems to highlight the quantitative relation between sequential intermediates which are assumed to emerge in the course of polypeptide chain folding.