An Introduction to Homology Modeling

Abstract

Homology modeling’, also known as comparative modeling or template-based modeling (TBM) refers to modeling a protein three-dimensional structure using a known experimentally determined structure of a homologous protein as a template. Identifying the protein structure has been the ultimate goal in protein modeling studies. Knowing the protein structure assists in the study of protein function and dynamics, generating in silico protein models, structure-based drug design, interaction with other ligands, antigenic behavior and rational designing. Homology modeling gives the researchers and scientists the structural information of proteins in situations when experimental techniques fail. Many proteins are simply too large for NMR analysis and cannot be crystallized for X-ray diffraction. Also, it provides the molecular biologists and biochemists with ‘low-resolution’ structures, containing information about the spatial arrangement of important residues in the protein macromolecules. Such information helps in designing of new set of experiments. As an example, the design of site-directed mutagenesis experiments can be significantly improvised using low-resolution model structures.