This paper is a little older (2011) but just recently came to my attention.
The study, by Gotze, et. al., details the construction and testing of StavroX a software package for studying enzymatically linked peptides with intact disulfide bridges. Following the development, the authors go on to show that the software works with three different biological systems. If you are interested in protein-protein interactions, you might want to check this out!
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