Step 4 Constructing Protein Models

Selection of a suitable template is very important the better the sequence identity (and similarity), the better the protein model. Here we selected hen s egg white lysozyme as the template in contrast to the other candidates explored by Browne et al., Perutz, and Perutz et Our selection 

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As mentioned, the construction of a protein model can be accomplished in six steps. Here we discuss each of those steps and explain several methodologies (applications) available for each. The most noticeable theme about a comparative modeling study is that some steps allow for many ways to complete the same task. For each step, only the most common methods will be discussed along with their advantages and disadvantages. 

The three protein model constructing methodologies discussed in this section use different conceptual means to construct a protein model. The refinement methodologies inherent to these methods were not discussed. In the section. Step 5 Refinement of Protein Models, the refinement of the raw output of these methods (the protein model) to further reduce steric clashes is described. 

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