Homology modeling: An outline of the method
The term "protein homology modeling", also called comparative modeling, refers to modeling a protein structure using a known experimentally determined structure of a homologous protein as a modeling template. In this chapter I will discuss the basics of homology modeling techniques, questions like: What can be modeled? How to find a template for homology modeling? What are the error sources in modeling? How to asses the quality of a homology model? A modeling tutorial with the use of the Swiss Model modeling server and resources, will show you how to make a homology model quickly and efficiently. Two cases are discussed, the first one is relatively easy modeling, while the second contains modeling of a multi-domain protein with 3 templates and fitting the domains to the final structure (will be finished soon!).Introduction
How to model
In the following two pages you will find a tutorial on the use of the SwissModel server for template identification and modeling. To learn the basics of the technique, this part will describe a relatively strait forward case of modeling.
Tutorial 1, part 1
Tutorial 1, part 2
In this tutorial I will discuss a more advanced case of modeling a multidomain protein, which requires domain identification, identification of templates for each domain separately and an attempt to reconstruct a protein using the different models.
Multidomain proteins, part 1
Multidomain proteins, part 2
Assessment of the quality of the homology model is very important to perform and should never be ignored. Here I will provide a discussion of the various aspects associated with the quality of the model.
Structure quality in homology modeling:
Error sources in modeling
Model energy estimation and relation to model quality:
Geometric and structural considerations: