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PoPS specifications

Information


Unique identifier OMICS_06954
Name PoPS
Alternative name Prediction of Protease Specificity
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for Prediction of Protease Specificity

PoPS citations

 (8)
library_books

Software aided approach to investigate peptide structure and metabolic susceptibility of amide bonds in peptide drugs based on high resolution mass spectrometry

2017
PLoS One
PMCID: 5665424
PMID: 29091918
DOI: 10.1371/journal.pone.0186461

[…] re developed to identify the most possible protease and/or the labile residues and the most likely cleavage site for the studied protein/peptide. However, these tools (SitePrediciting [], PROSPER [], PoPS [], PeptideCutter []) are based on available literature or rely on the MEROPS database and therefore are limited to the 20 standard amino acids [] and thus do not properly cover unnatural amino a […]

library_books

Block based characterization of protease specificity from substrate sequence profile

2017
BMC Bioinformatics
PMCID: 5627433
PMID: 28974219
DOI: 10.1186/s12859-017-1851-1

[…] ate-sequence information to specificities of proteases to highlight the enzymatic preferences, especially for specific catalytic types []. Integrating features of substrate sequences characteristics, PoPS [] and PROSPER [] are proposed to predict protease substrate cleavage sites. A well-designed approach of identifying the specificity of the protease will contribute to a better method of predicti […]

library_books

Profiling the Extended Cleavage Specificity of the House Dust Mite Protease Allergens Der p 1, Der p 3 and Der p 6 for the Prediction of New Cell Surface Protein Substrates

2017
Int J Mol Sci
PMCID: 5535866
PMID: 28654001
DOI: 10.3390/ijms18071373

[…] obability of amino acid x occurring in a given library and n is the total number of sequences analyzed.Related standard deviations Δσ were then normalized to the range −5.0 to +5.0 as required by the PoPS interface []. Specificity matrices for Der p 1, Der p 3 and Der p 6 were modeled and used to screen, among the human proteome, new potential cell surface protein substrates targeted by these HDM […]

library_books

Proteolytic inactivation of nuclear alarmin high mobility group box 1 by complement protease C1s during apoptosis

2016
PMCID: 5018544
PMID: 27648302
DOI: 10.1038/cddiscovery.2016.69

[…] The Web-based PoPS software (http://pops.csse.monash.edu.au/) was used to predict C1s cleavage sites on HMGB1., The C1s cleavage site encompassed eight residues with a core arginine residue recognized by the S1 sub […]

library_books

Analysis of the minimal specificity of caspase 2 and identification of Ac VDTTD AFC as a caspase 2 selective peptide substrate

2014
Biosci Rep
PMCID: 3966047
PMID: 27919034
DOI: 10.1042/BSR20140025

[…] scribed [,]. Weighted P4–P2 transcriptional reporter data were used to generate a matrix model (Supplementary Table S1; available at http://www.bioscirep.org/bsr/034/bsr034e100add.htm). The Web-based PoPS program [] was used to screen the National Center for Biotechnology Information (NCBI) protein database for potential substrates. […]

library_books

PROSPER: An Integrated Feature Based Tool for Predicting Protease Substrate Cleavage Sites

2012
PLoS One
PMCID: 3510211
PMID: 23209700
DOI: 10.1371/journal.pone.0050300

[…] In recent years, several general tools have been developed to predict cleavage sites for various proteases, such as PoPS and SitePrediction . To objectively compare the prediction results, we first tested these three tools on the same training and testing datasets, based in turn on the compiled substrate datasets. […]

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PoPS institution(s)
School of Computer Science and Software Engineering and The Victorian Bioinformatics, Consortium, Monash University, Melbourne, Victoria, Australia

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