The alignment tool allows you to fold the current protein to be like a protein that has a known structure. As scientists perform x-ray crystallography images of real proteins, they add them to a database. These proteins have a known lowest energy state structure. Proteins that are similar to the current protein are listed in the Alignment Tool. The matching of a protein to an existing alignment is called threading. Select the protein that is most similar to the protein at the top by placing a check mark next to it, and click the happy face button. Alignment Tool legend