Step 1 Searching for Related Sequences and Structures

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. 

It is estimated that the amount of genomic data collected and analyzed doubles yearly. Without suitable databases, it would be difficult to use the results of genome sequencing. The journal Nucleic Acids Research publishes an aimual database issue with reviews covering all databases freely available (the exception being for databases that provide limited access for those who choose not to register). Those databases provide annotation-based searches with the option (links to other websites) to perform sequence similarity 

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