Protein homology modeling steps

The aim of the second dimension depth is to consider protein 3D-stmctures to uncover structure-function relationships. Starting from the protein sequences, the steps in the depth dimension are structure prediction, homology modeling of protein structures, and the simulation of protein-protein interactions and ligand-complexes. 

Figure 4 Steps in homology modeling of protein structure. Modeling the structure of a protein by considering its homology to known homologs is one of the most effective methods of structure-prediction. The critical steps are the identification and alignment of the target sequence to the template sequence (1) and (2).

What does this have to do with structure prediction In fact, we would like to solve a fold recognition problem (Fig. 7.3). For each domain, we consider several million possible sequences, and identify the most favorable. These provide a signature of the 3D domain structure, or fold. Indeed, if we consider a new protein sequence, for which the 3D structure is unknown, we can compare it to our database of computed sequences. If the new sequence is similar to one or more in our database, we can infer that it will adopt the same 3D stmcture. In effect, we have identified the fold of the new sequence, and this is the first step towards structure prediction by homology modeling (above) [7]. 

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