ProP protocols

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ProP specifications

Information


Unique identifier OMICS_02445
Name ProP
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Nikolaj Blom <>

Publication for ProP

ProP in pipelines

 (4)
2017
PMCID: 5412055
PMID: 28464870
DOI: 10.1186/s12864-017-3699-1

[…] or more cysteine residues in the predicted mature protein were also identified. ssps were screened for repeat content using radar [–]. the presence of pro-peptide cleavage sites was analysed using prop 1.0 [], with those sites with a score ≥0.5 recorded as positive. interproscan 5 [, ] was used to analyse conserved domains in the ssps., in addition to the orthomcl analysis, the ssps (≤200 aa […]

2015
PMCID: 4558851
PMID: 26201648
DOI: 10.1093/gbe/evv133

[…] peptide was detected with signalp 4.0 (), and discriminated from transmembrane domains with phobius (). potential sites of posttranslational proprotein convertase cleavage were identified with prop 1.0 (). possible posttranslational c-terminal cleavage sites by carboxypeptidase e or by peptidylglycine, α-amidating monooxygenase were detected with elm (). the subcellular localization […]

2013
PMCID: 3545927
PMID: 23335997
DOI: 10.1371/journal.pone.0054290

[…] “hypothetical” and “predicted” by ncbi. we also removed mitochondrial proteins because they normally are not processed by furin . the resulting set of 23,348 individual proteins was screened using prop, an artificial neural network program , to identify sequences containing the cleavage motif (k/r)-(x)n-(k/r)↓ (where n is 0, 1, 2, 4 or 6 and x is any amino acid). the software identified 13,736 […]

2011
PMCID: 3244413
PMID: 22216098
DOI: 10.1371/journal.pone.0028525

[…] deducted protein sequences were also sent to the signalp server, to the tmhmm server to detect membrane helices, the netoglyc server to detect possible mucin-type galactosylations and to the prop server to identify putative furin-processed protein cleavage sites. the protein sequences in were also clusterized progressively from 25% similarity to 99% similarity over 50% of the length […]


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ProP in publications

 (29)
PMCID: 5853523
PMID: 29556470
DOI: 10.1016/j.ijppaw.2018.01.004

[…] human c. viatorum subtypes was made using mafft in geneious (). a table of pairwise amino acid similarities amongst c. viatorum subtypes was also constructed using geneious (). the online servers prop 1.0 (www.cbs.dtu.dk/services/prop/) (), netnglyc 1.0 (www.cbs.dtu.dk/services/netnglyc/) () and netoglyc 4.0 (www.cbs.dtu.dk/services/netoglyc/) () were used to predict furin cleavage sites, […]

PMCID: 5614858
PMID: 28846083
DOI: 10.1038/nn.4630

[…] and cadherin processing,. we identified putative furin cleavage sites in mab-20/sema, unc-6/netrin and fmi-1/flamingo proteins using an rxxr consensus motif, or cleavage sites predicted by the prop1.0 algorithm (, , ). a single predicted site in mab-20 fulfills both criteria and is conserved in vertebrate semaphorin homologs. mutation of the conserved arginine (r247h) using crispr/cas9 […]

PMCID: 5549699
PMID: 28792526
DOI: 10.1371/journal.pone.0182395

[…] representative spectrum annotated by glycresoft (one of 345) submitted to the proteomexchange consortium []., the furin-like protease site that separates gp40/gp15 was predicted by the online tool “prop 1.0 server”, made available by the center for biological sequence analysis, department of systems biology, technical university of denmark (www.cbs.dtu.dk/services/prop/) []. signal peptides […]

PMCID: 5612097
PMID: 28751378
DOI: 10.1074/jbc.M117.797811

[…] by extracellular proteases, such as dispase, to yield the 38-kda active form (, ), we assumed a similar activation mechanism for the hypothetical k. albida microbial transglutaminase and used the prop 1.0 server to analyze the probability for signal and propeptide sequences in the n-terminal region of the protein (supplemental fig. 1b). vaaptpr↓ap was the only predicted propeptide cleavage […]

PMCID: 5446729
PMID: 28549438
DOI: 10.1186/s12985-017-0766-9

[…] data bank (pdb) and predicted using a web-based swiss-model server. the cleavage sites in the s protein were predicted by comparing amino acid sequences, combined with analysis using a web-based prop server []. phylogenetic trees were constructed using the maximum-likelihood (ml) algorithm, with bootstrap values determined by 1000 replicates in mega6 and phyml software [, ]., a total of 177 […]


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