From Protein Structure to Function with Bioinformatics.pdf

Chapter 1Ab Initio Protein Structure PredictionJooyoung Lee, Sitao Wu, and Yang ZhangAbstract Predicting protein 3D structures from the amino acid sequence stillremains as an unsolved problem after five decades of efforts. If the target proteinhas a homologue already solved, the task is relatively easy and high-resolutionmodels can be built by copying the framework of the solved structure. However,such a modelling procedure does not help answer the question of how and why aprotein adopts its specific structure. If structure homologues (occasionally analogues)do not exist, or exist but cannot be identified, models have to be constructedfrom scratch. This procedure, called ab initio modelling, is essential for a completesolution to the protein structure prediction problem; it can also help us understandthe physicochemical principle of how proteins fold in nature. Currently, the accuracyof ab initio modelling is low and the success is limited to small proteins (