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Protocols

PAProC specifications

Information


Unique identifier OMICS_05750
Name PAProC
Alternative name Prediction Algorithm for Proteasomal Cleavages
Interface Web user interface
Restrictions to use None
Computer skills Basic
Version 1.2
Stability Stable
Maintained Yes

Taxon


  • Plants and Fungi
    • Saccharomyces cerevisiae
  • Primates
    • Homo sapiens

Publications for Prediction Algorithm for Proteasomal Cleavages

PAProC citations

 (21)
library_books

Genome Wide Association Study Identifying Candidate Genes Influencing Important Agronomic Traits of Flax (Linum usitatissimum L.) Using SLAF seq

2018
Front Plant Sci
PMCID: 5767239
PMID: 29375606
DOI: 10.3389/fpls.2017.02232

[…] Based on the restriction analysis of PAProC (http://www.paproc.de/) (Nussbaum et al., ), DNA fragments of 500–580 bp were gel purified and PCR amplified using a forward primer (5′-AATGATACGGCGACCACCGA-3′) and a reverse primer (5′-CAAGCAG […]

library_books

Immunoinformatics Approach in Designing Epitope based Vaccine Against Meningitis inducing Bacteria (Streptococcus pneumoniae, Neisseria meningitidis, and Haemophilus influenzae Type b)

2016
PMCID: 5091093
PMID: 27812281
DOI: 10.4137/DTI.S38458

[…] proteasomal recognition site is not favorable as an epitope vaccine candidate because it will be degraded during antigen processing. The determination of proteasomal cleavage site was conducted using PAProC. Fragments having ≥9 amino acid residues were used for further analysis of TAP binding preference (). TAP binding preference has significant influence in selecting T-cell epitopes because antig […]

library_books

Vaccine Design for H5N1 Based on B and T cell Epitope Predictions

2016
Bioinform Biol Insights
PMCID: 4852757
PMID: 27147821
DOI: 10.4137/BBI.S38378

[…] Following Velkov et al, the mapping of our epitopes has taken into account their tendency of antigenic drifting. The prediction of proteosomal cleavage H5N1 virus was analyzed by using PAPROC-I tools (http://www.paproc.de/), while the transport antigen presentation (TAP) binding was predicted by using TAPPRED server (http://www.imtech.res.in/raghava/tappred/)., Propred and netMHCpan […]

library_books

Immunoinformatics and epitope prediction in the age of genomic medicine

2015
Genome Med
PMCID: 4654883
PMID: 26589500
DOI: 10.1186/s13073-015-0245-0

[…] rect evidence from naturally presented HLA class I epitopes is most commonly used for in vivo prediction. Predictors for in vitro cleavage are netChop 20S [], PCM [], FragPredict [], Pcleavage [] and PAProC []. Owing to the scarcity of data, few predictors for in vivo cleavage are available. The two most popular predictors are netChop Cterm [] and ProteaSMM []. The first benchmark for proteasomal […]

library_books

Epitope Prediction Assays Combined with Validation Assays Strongly Narrows down Putative Cytotoxic T Lymphocyte Epitopes

2015
PMCID: 4494349
PMID: 26343185
DOI: 10.3390/vaccines3020203

[…] Under physiological conditions, proteins have to be cleaved by proteasomes into short peptides in order to be loaded onto MHC class I molecules. Proteasomal cleavage sites were predicted with MAPPP, PAProC I and Netchop. MAPPP and Netchop predict the cleavage site of constitutive proteasomes and PAProC I predicts cleavage site of both constitutive proteasomes and immunoproteasomes. From the resul […]

library_books

Role of peptide processing predictions in T cell epitope identification: contribution of different prediction programs

2014
Immunogenetics
PMCID: 4297296
PMID: 25475908
DOI: 10.1007/s00251-014-0815-0

[…] l. ; Nielsen et al. ; Tenzer et al. ; Ginodi et al. ; Kuttler et al. ; Nussbaum et al. . Most predictors, e.g., FragPredict (Holzhutter et al. ; Holzhutter and Kloetzel ), ProteaSMM (Tenzer et al. ), PAProC (Kuttler et al. ; Nussbaum et al. ), and PepCleave (Ginodi et al. ), have been trained on the in vitro proteasome digestion data from β-casein and enolase (Emmerich et al. ; Toes et al. ). NetC […]

Citations

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PAProC institution(s)
Universität Tübingen, Interfakultäres Institut für Zellbiologie, Abteilung Immunologie, Tübingen, Germany; Universität Tübingen, Biomathematik, Tübingen, Germany

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