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

Partial Threading - step by step 

Blog entry: Comparative Modeling Tools for Structure Prediction The Alignment Tool: Purpose and Prospects

Science behind : Homology modeling

Partial Threading[edit | edit source]

Partial threading allows the threading of just a part of one of the lower proteins. Using this you can grab different parts of different proteins and thread them.

  1. Select the part of the your protein on the first line, by clicking on an amino acid, then shift-clicking on another one.
  2. There are two boxes on the upper right of the dialog, click the left of these boxes.
  3. Put a check mark next to the protein you want to partial thread to.
  4. Click the happy face button.

For example, you might want to do this if the template you threaded to has a poor match to the native structure in some part of the protein. A poor match is indicated by a lack of white lines under the top line in the alignment tool. Look for another template with more white lines in the area and select that part on the first line and partial thread as above. For example, a protein might have a poor match to a helix and after the initial threading you can see that the helix structure is not recognised, but another template might have the helix structure matched. You can either fix these matching problems by hand or get the shape right immediately with partial threading. Don't select too small a region for partial threading or it won't work.

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