In silico digestion

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In silico digestion mvm35  2024-09-24 08:19
 

For in silico digestion using various enzyme.

What do the following mean (X= some amino acid):

[X | P]
[X | - ]
[- | X]

thank you.

 
 
Nick Shulman responded:  2024-09-24 08:32
[X | P] means "cleave at amino acid X unless followed by P
[X | - ] means "cleave at amino acid X regardless of what comes next
These are both for C-terminal enzymes which cleave after the specified specified enzyme.

[- | X] is something that you would only see for N-terminal enzymes and means "cleave at the N-terminal of X regardless of what amino acid comes before it".

When you are on the "Digestion" tab at "Settings > Peptide Settings" you can choose "<Edit list...>" from the Enzyme dropdown and then if you Edit any of the items it will display the Edit Enzyme dialog which has more words on it saying what the enzyme does.
-- Nick