Comparative modeling alignment

All current comparative modeling methods consist of four sequential steps (Fig. 2) [5,6]. The first step is to identify the proteins with known 3D structures that are related to the target sequence. The second step is to align them with the target sequence and pick those known structures that will be used as templates. The third step is to build the model... 

Figure 12 ModBase, a database of comparative protein stracture models. Screenshots of the following ModBase panels are shown A form for searching for the models of a given protein, summary of the search results, summary of the models of a given protein, details about a single model, alignment on which a given model was based, 3D model displayed by RASMOL [237], and a model evaluation by the Prosall profile [217],...

Fig. 10. Case study mD-QSAR methods 4D-QSAR. Two models (Models 2 and 4) are compared for Alignment 1. The only difference between the models is the two erroneous descriptors near the ethylamine of the compound. These two descriptors (3, -1, -1, any) and (3, -3, -2, any), for Models 2 and 4, respectively, provide misleading results.

The comparative modeling approach has been reviewed in detail. The process begins with the identification of known structures related to the sequence to be modeled. A sequence alignment is then constructed. A model of the backbone... 

A. S. Yang, B. Honig. Sequence to structure alignment in comparative modeling using PrISM. Proteins. 1999, 37, 66-72. 

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