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Documentation for PeptideCutter Peptide Characterisation Software:

1. Introduction:

PeptideCutter searches a protein sequence from the SWISS-PROT and/or TrEMBL databases or a user-entered protein sequence for protease cleavage sites. Single proteases and chemicals, a selection or the whole list of proteases and chemicals can be used. Different forms of output of the results are available: Tables of cleavage sites either grouped alphabetically according to enzyme names or sequentially according to the amino acid number. A third option for output is a map of cleavage sites. The sequence and the cleavage sites mapped onto it are grouped in blocks, the size of which can be chosen by the user to provide a convenient form of print-out.

2. Using PeptideCutter:

In the program there are a number of fields that must be filled in. In the following, these fields are described, from the top of the form to the bottom.

2.1. Protein Sequence to be Cleaved

In order to provide the program with a sequence the full sequence can be transfered into the first textbox. Alternatively, an identifier or an accession number for a protein sequence stocked in the SWISS-Prot or the TrEMBL database can be entered.

2.2. Enzymes or Reagents to Use for Cleavage

All or a group of favourite enzymes and chemicals can be selected. Most of the cleavage rules for individual enzymes were deduced from specificity data summed up by Keil (1992). Please be aware of the fact, that in most cases, the PeptideCutter program makes use of relatively simple rules.
Only in few cases, specificity data allowed the establishment of more sophisticated models, e.g. for trypsin or chymotrypsin. In this case, the cleavage probability of the individual sites is added to the results.

2.3. Display of results

Different options for the result display are available:
The first two options imply the creation of a list of all detected cleavages. The sequence map is displayed in portions of 10 to 60 amino acids. It is possible to modify the portion size and thus the map output according to his needs. Adjusting this size may be especially important when printing out the map. In addition to this, it is possible to consider only enzymes for the output that cut the sequence a chosen number of times. When the results are displayed in form of a map, one enzyme of choice can be selected by mouseclicking. The sites that are potentially cleaved by this enzymes are then displayed in a separate window.