Model building by homology

Is easy id predict the structure of a point mutant. They also determined a set of simple rules that can be used to predict the structure of a mutated residue given the structure of the wH4 ypc protein. These rules are described in Figure 3. It is to be expected—although it is not yet proven—that this simple scheme can be extrapolated to model building by homology in cases of high homology. 

L. Holm, C. Sander. Fast and simple Monte Carlo algorithm for side chain optimization in proteins Application to model building by homology. Proteins. 1992, 14, 213-223. 

G. Chinea, G. Padron, R. W. Hooft, C. Sander, G. Vriend. The use of position-specific rotamers in model building by homology. Proteins. 1995, 23, 415-421. 

All models built by homology will have errors. Side chains can be placed incorrectly, or whole loops can be misplaced. As with most errors, they become less of a problem when they can be localized. For example, looking at an enzyme it is usually not important that a loop far away from the active site be modeled incorrectly. The most important step in the process of model building by homology is therefore undoubtedly the verification of the model, and the estimation of the likelihood and magnitude of errors. 

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