UbPred

[…] egfr, gsk3, insr, pka, pkb, pkc, pkg, rsk, src, cdc2, cdk5 and p38mapk. server at: http://www.cbs.dtu.dk/services/netphos/., predictor of protein ubiquitination sites (). server at: http://www.ubpred.org/. ubpred is a random forest-based predictor of potential ubiquitination sites in proteins. it was trained on a combined set of 266 non-redundant experimentally verified ubiquitination […]

[…] with a 2.64 cut-off value was selected for sumosp 2.0 analysis, respectively (gill, ; xue et al., ). whereas, putative ubiquitylation sites were predicted by using bdm-pub (bdmpub.biocuckoo.org) and ubpred (www.ubpred.org) programs (radivojac et al., ). for bdm-pub, the only balanced cut-off value option was taken and in case of ubpred, the lysine amino acid having 0.62 score was considered […]

[…] . tm-align was used to calculate tm-scores and root mean square deviation (rmsd) (http://zhanglab.ccmb.med.umich.edu/tm-align/) ., putative ubiquitylation sites were predicted using the ubpred (www.ubpred.org) and bdm-pub (bdmpub.biocuckoo.org) programs . in ubpred, lysine residues with a score of ≥0.62 were considered ubiquitylated. for bdm-pub, the balanced cut-off option […]

[…] 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 […]

[…] 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, […]

[…] 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 […]

[…] 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 […]

[…] 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 […]