I have amino acid sequence of some aspartic acid proteases (not very common) from fungus. I want to check the specific restriction sites of these proteases on some known substrates using in silico tools. Do anybody have idea about some tools/softwares which can give me predicted restriction sites for particular en
Normal sequence-based prediction tools rely on the known specificities of well characterized proteases (e.g http://web.expasy.org/peptide_cutter/, https://prosper.erc.monash.edu.au/methodology.html). In the case of an uncommon protease I don't think these would give good results - is your aspartic protease close enough in sequence to any aspartic protease structure in the structure database that a reasonable homology model can be built. Analysis of the sequence differences in the peptide binding cleft may help you to decide whether your protease should show a similar pattern or in what direction it might deviate. On the experimental side, library-based methods facilitate the characterization of the cleavage pattern of novel proteases: Article Turk BE, Huang LL, Piro ET, Cantley LCDetermination of prote...
Thanks for answer. I tried both tools and as you mentioned the proteases I'm working are not in the list of either in peptide cutter or in prosper. I will read the publication and try to understand the other mechanism. thanks anyways.
Here is another interesting proteomics-type approach to determining which substrates actually get cleaved:
Article Global Analysis of Cellular Proteolysis by Selective Enzymat...
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