Comparative Protein Structure Modeling: Introduction and Practical Examples with Modeller

A useful three-dimensional (3D) model for a protein of unknown structure (the target) can frequently be built based on one or more related proteins of known structure (the templates). This is the aim of comparative or homology protein structure modeling. The necessary conditions are that the similarity between the target sequence and the template structures is detectable and that the correct alignment between them can be constructed. For reviews of comparative modeling, see refs. , , , , . This approach to structure prediction is possible because a small change in the protein sequence usually results in a small change in its 3D structure (,).