Computational Modeling of Protein Three-Dimensional Structure: Methods and Resources

Abstract

Abstract Proteins are complex macromolecules involved in essential biological processes in a living organism. Determining the three-dimensional structure of the protein is central to understand its functional role at the molecular level. Experimental approaches such as X-ray crystallography, nuclear magnetic resonance, and cryogenic electron microscopy have been developed by researchers to solve the protein structures. However, the high-cost and effort-intensive nature associated with these methods is limiting their usage for deciphering protein structures. Thus, as an alternative, the development of computational methods to model protein structure has gained importance to the scientific community. The existing computational methods can be broadly classified into two major categories, namely, the template-based (homology modeling and threading) and the template-free modeling (ab initio). This chapter provides an overview of the available computational approaches for modeling protein structures along with various relevant resources and case study of the widely used methods.