An Insight of Protein Structure Predictions Using Homology Modeling

The homology modeling is the computational method, and it is one of the essential steps to construct the 3D protein structure using the query sequences of amino acid and template protein. If the query sequence has similar with template structure, then the model structure can be easily predicted with high resolution. The homology modeling for structural prediction plays a crucial role to discover the novel drug target against the various diseases. Based on the two important principles such as laws of physics and evolution, the 3D protein structure can be predicted. According to the physical and evaluation principles, protein folds have stable and well-formed structure via minimizing the energy and protein molecule has outcome of gradual changes in sequence and structure. The homology modeling has different multi steps which are most accurate to predict the absolute model structure. When the sequence identity is below 15%, it cannot be used for further structure modeling which could be lead to deceptive conclusion. The maximum similarity between 30% and 40% obtained from the query and template sequences can be considered for further homology modeling. If the similarity is above 50%, then the obtained model is adequate quality which can be used for further molecular docking for protein-protein docking, protein-ligand complexes, and molecular dynamic simulation studies. This modeling technique is very comfortable, faster, and cost-effective. This chapter will discuss the different homology model for the prediction of protein structure for the drug development process.