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UbiProber specifications

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Unique identifier OMICS_05547
Name UbiProber
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained No

Publication for UbiProber

UbiProber citations

 (8)
library_books

RNF138 mediated ubiquitination of rpS3 is required for resistance of glioblastoma cells to radiation induced apoptosis

2018
PMCID: 5799804
PMID: 29371697
DOI: 10.1038/emm.2017.247

[…] ination sites, based on the three-dimensional structure of rpS3 (Protein Data Bank ID: 3KC4) and prediction results from the ubiquitination prediction database (PhosphoSitePlus, UbPred, iUbiq-Lys and UbiProber), we mutated six Lys residues (K10, K90, K151, K202, K214 and K227) to Ala and measured radiation-induced poly-ubiquitination (). This analysis revealed a ubiquitin modification of rpS3 at a […]

library_books

Lys48 ubiquitination during the intraerythrocytic cycle of the rodent malaria parasite, Plasmodium chabaudi

2017
PLoS One
PMCID: 5467854
PMID: 28604779
DOI: 10.1371/journal.pone.0176533

[…] t-translational modification in this parasite. Notably, some of the P. chabaudi experimentally detected ubiquitinated proteins were not predicted in silico by the available software such as UbPred or UbiProber, suggesting that the recognition elements could be species-specific.As in other Plasmodium species, P. chabaudi has three genes related to ubiquitin and its polyubiquitin sequence is highly […]

library_books

Protein post translational modifications: In silico prediction tools and molecular modeling

2017
Comput Struct Biotechnol J
PMCID: 5397102
PMID: 28458782
DOI: 10.1016/j.csbj.2017.03.004

[…] n a support vector machine algorithm (SVM), which allows studying the correlation between ubiquitylation and protein half-life. In order to overcome the lack of accuracy and training data deficiency, UbiProber and iUbiq were designed (). UbiProber predicts both general and species-specific ubiquitylation sites using large-scale experimental data as training set, while iUbiq is based on evolution […]

library_books

Impact of novel SNPs identified in Cynara cardunculus genes on functionality of proteins regulating phenylpropanoid pathway and their association with biological activities

2017
BMC Genomics
PMCID: 5314637
PMID: 28212611
DOI: 10.1186/s12864-017-3534-8

[…] t SNP influence in post-translational modifications (PTM) several programs were used, namely for phosphorylation, SUMOylation, ubiquitination and methylation: NetPhos 2.0 [], SUMOplotâ„¢, UbPred [] and UbiProber [] and MeMo 2.0 [] were used, respectively. […]

library_books

Post translational regulation of the cleaved fragment of Par 4 in ovarian and endometrial cancer cells

2016
Oncotarget
PMCID: 5095052
PMID: 27175591
DOI: 10.18632/oncotarget.9235

[…] icted the K333 site using proteomic discovery-mode mass spectrometry, thus strengthening the likelihood of a true ubiquitination site [, ]. In parallel, we used three additional bioinformatics tools (Ubiprober, Ubpred, BDM-PUB) and identified 13 candidate ubiquitination sites, including the K333 site previously predicted by discovery-mode mass spectrometry (Table ) [–]. By looking at the position […]

library_books

Computational methods for ubiquitination site prediction using physicochemical properties of protein sequences

2016
BMC Bioinformatics
PMCID: 4778322
PMID: 26940649
DOI: 10.1186/s12859-016-0959-z

[…] fiers (i.e., the one based on binary amino acid encoding and the one based on the AAindex [] physicochemical property encoding) using Logistic Regression (LR) []. Chen et al presented a tool known as UbiProber for large scale predictions of ubiquitination based on SVM technique using three features of K nearest neighbor, AA composition, and PCP []. Walsh et al designed a sequence-based ubiquitinat […]


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UbiProber institution(s)
Department of Chemistry, Nanchang University, Nanchang, China

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