Protein Design: Computational Methods

This lecture introduces the field of computational protein design, covering challenges in protein structure prediction, energy functions for scoring structures, search algorithms for sampling structures, and applications in synthetic biology and biomedicine. The importance of protein design is highlighted due to proteins being essential for cellular functions. The lecture explains the process of reengineering natural proteins through amino acid substitutions, designing proteins from scratch, and the challenges faced in designing proteins. Various computational and experimental methods for protein design are discussed, including random mutagenesis, directed evolution, and the use of rotamer libraries. The lecture also explores the concept of energy landscapes in protein conformational space and the role of Monte Carlo simulations in protein structure refinement.