PeptideCutter protocols

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PeptideCutter specifications

Information


Unique identifier OMICS_11634
Name PeptideCutter
Interface Web user interface
Restrictions to use None
Input data 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.
Output data 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.
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


PeptideCutter in pipeline

2010
PMCID: 2935394
PMID: 20838648
DOI: 10.1371/journal.pntd.0000813

[…] the presence of signal peptide, netnglyc 1.0 and netoglyc 3.1 (http://www.cbs.dtu.dk/services/) to predict potential glycosylation sites. putative proteolytic cleavage sites were predicted using peptidecutter (http://www.expasy.ch/tools/peptidecutter/) program. protein domain searches were performed using smart (http://smart.embl-heidelberg.de/). an unrooted phylogenetic tree was constructed […]


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PeptideCutter in publications

 (70)
PMCID: 5883307
PMID: 29614969
DOI: 10.1186/s12868-018-0420-5

[…] activity appears to not be involved in the 27-ohc-induced increase in α-syn protein levels we determined the potential role of 27-ohc in inhibiting the degradation of α-syn protein using expasy peptidecutter, a tool that predicts potential cleavage sites cleaved by proteases in a given protein sequence. our data shows that both 27-ohc and the proteasomal inhibitor mg132 reduce caspase-like […]

PMCID: 5883421
PMID: 29615132
DOI: 10.1186/s40478-018-0527-z

[…] 50 kda) could be detected on immunoblots. this form matches with the truncated fragment of sphk2 cleaved by caspase-1 at the level of the d138 according to weigert et al., and online software expasy (peptidecutter) []. in this truncated fragment, all the domains of sphk2 are preserved including the catalytic domain and the ligand binding domain, suggesting that cleaved sphk2 could preserve its enz […]

PMCID: 5877670
PMID: 29534491
DOI: 10.3390/ijms19030809

[…] while subsurface regions remain protected. no complete digestion of exti was observed after the treatment, even with increased concentrations up to 30 mg/ml of proteinase k (b), although the peptidecutter program [] predicted 206 proteinase k cutting sites in the exti sequence. in contrast, severe degradation of the total protein, dependent on the increased amount of proteinase k, […]

PMCID: 5844913
PMID: 29556505
DOI: 10.3389/fvets.2018.00040

[…] of higher molecular weight native proteins, occurred during ovi t.e. antigen purification and preparation for sds-page, carried out without using protease inhibitors. this was confirmed by expasy peptidecutter analysis that predicted several potential cleavage sites for proteases or chemicals in the sequence of all the proteins. the 24 unique proteins with molecular weight lower than 37 kda […]

PMCID: 5829226
PMID: 29487296
DOI: 10.1038/s41467-018-03153-8

[…] acid in 50% acetonitrile with 0.1% tfa) directly onto a maldi-tof plate for subsequent analysis. the molecular weight of the expected peptide fragments before and after digestion was predicted using peptidecutter (expasy bioinformatics portal, swiss institute of bioinformatics). peptide fragment containing the n-terminal group was examined for modification., maldi-tof measurements were recorded […]


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