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UbPred specifications

Information


Unique identifier OMICS_05546
Name UbPred
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for UbPred

UbPred citations

 (64)
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

[…] these Lys are ubiquitination 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 mod […]

library_books

Decoding the network of Trypanosoma brucei proteins that determines sensitivity to apolipoprotein L1

2018
PLoS Pathog
PMCID: 5790291
PMID: 29346416
DOI: 10.1371/journal.ppat.1006855

[…] ts that ubiquitination may contribute to T. b. brucei apoL1 sensitivity. At present, it is unclear which parasite proteins are modified and how this influences apoL1 action. However, using the online UbPred algorithm [] we identified high confidence candidate ubiquitination sites in 23 of the 63 top hits identified following apoL1 selection of our BSF T. b. brucei RNAi library (). Therefore, chang […]

library_books

Identification and in silico analysis of functional SNPs of human TAGAP protein: A comprehensive study

2018
PLoS One
PMCID: 5766082
PMID: 29329296
DOI: 10.1371/journal.pone.0188143

[…] Ubiquitylation is a PTM which serves as a degradation mechanism for proteins and helps in DNA damage repair []. These modification sites in the TAGAP were predicted by UbPred and BDM-PUB tools. UbPred predicted 12 lysine residues in the TAGAP protein that experience ubiquitylation while BDM-PUB predicted that 33 lysine residues undergo ubiquitylation. Total 10 resid […]

library_books

Stabilization of phosphofructokinase 1 platelet isoform by AKT promotes tumorigenesis

2017
Nat Commun
PMCID: 5643558
PMID: 29038421
DOI: 10.1038/s41467-017-00906-9

[…] H33W), indicating that E3 ligase activity of TRIM21 is required for PFKP ubiquitylation and degradation.To identify the ubiquitylation residue of PFKP, we analyzed the PFKP sequence using the webtool UbPred: predictor of protein ubiquitylation sites (http://www.ubpred.org/) and found that the K10 may have been ubiquitylated (Supplementary Table ). The PFKP K10R mutant showed complete resistance to […]

library_books

TRIM29 promotes DNA virus infections by inhibiting innate immune response

2017
Nat Commun
PMCID: 5643338
PMID: 29038422
DOI: 10.1038/s41467-017-00101-w

[…] STING contains nine lysine residues. Eight of these (Lys20, Lys137, Lys150, Lys224, Lys236, Lys347, and Lys370) were predicted to be possible ubiquitination sites with high confidence scores by the UbPred program that predicts such sites or reported previously (Supplementary Table ). To determine the STING-ubiquitination sites, we replaced each of those STING lysine residues noted above individu […]

library_books

Deciphering the Role of CBF/DREB Transcription Factors and Dehydrins in Maintaining the Quality of Table Grapes cv. Autumn Royal Treated with High CO2 Levels and Stored at 0°C

2017
Front Plant Sci
PMCID: 5609105
PMID: 28970842
DOI: 10.3389/fpls.2017.01591

[…] tiple alignment analysis was performed at the Swiss EMBnet node web server using ClustalW and BoxShade tools, respectively. The prediction of ubiquitination and sumoylation sites was performed using, UbPred () and SUMOsp2.0 servers (), respectively. The proline (P) glutamic acid (E) serine (S) threonine (T) (PEST) regions in the proteins were found using the EMBOSS program pestfind with the defaul […]

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UbPred institution(s)
School of Informatics, Indiana University, Bloomington, IN, USA

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