Server at Davidson College

Finds the combination of proteases that results in the smallest fragment
for the amino acid that is being targeted.

This tool allows the user to enter an amino acid sequence and an amino acid to target.
The user is digesting the protein using proteases and trying to obtain the smallest
fragment of amino acids around their targeted amino acid as possible. There is a list
of proteases that the user can choose from to try, or they can choose to try every
protease in the list. It is possible that the best choice (resulting in the smallest
fragment) is to simply use one protease. It is also possible that the best possibility
is a pair. Sometimes switching the order of digestions of the pair of proteases will
result in different fragments.

Click to download the list of protease cleavage sites (gathered from Table 1 of Biomolecules
journal, Research Applications of Proteolytic Enzymes in Molecular Biology).

* Protease
Enter the proteases you would like to try (You MUST select the "All" button if you want to try combinations of all the proteases in the list OR the "Selection" button if you want to choose from the list of proteases:
Selection (For multiple: hold down Ctrl for PC, Command for Mac)

* Amino acid sequence:

* Enter the index of the amino acid that you want to target (as an integer):

* Enter the number of possible sequences you want (as an integer):

* = required


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