UbiBrowser 2.0 is a comprehensive resource for proteome-wide known and predicted ubiquitin ligase (E3)/deubiquitinase (DUB) - substrate interactions in eukaryotic species. These E3/DUB-substrate interactions are derived from five data sources: manual curation, protein GO annotation, protein domain, protein motif and network topology.
A computational framework developed by us (Nature Communications, 2017, 8) was used to combine multiple biological evidences to generate a confidence score for the derived proteome-wide ubiquitin ligase (E3)/deubiquitinase (DUB)-substrate interactions in 39 eukaryotic species.More..
Notice: Due to the update of our prediction system, there is some difference between the predicted human ESIs results in UbiBrowser 2.0 and those in UbiBrowser 1.0. To make our prediction results reproducible, we provide the link to our previous UbiBrowser 1.0 website. You can use the human ESI prediction results from either UbiBrowser 1.0 or 2.0, because all of them were supported by certain biological evidences. Sorry for the possible confusion.
UbiBrowser 2.0 was developed at Beijing proteome research center (BPRC).
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Wang X, Li Y, He M, Kong X, Jiang P, Liu X, Diao L, Zhang X, Li H, Ling X, Xia S, Liu Z, Liu Y, Cui C, Wang Y, Tang L, Zhang L, He F, and Li D. UbiBrowser 2.0: a comprehensive resource for proteome-wide ubiquitin ligase/deubiquitinase-substrate interactions in eukaryotic species. Nucleic Acids Research. 2022, 50： D719–D728. Link to NAR website    BioArtMED news (Chinese)
Li Y, Xie P, Lu L, Wang J, Diao L, Liu Z, Guo F, He Y, Liu Y, Huang Q, Liang H, Li D, He F. An integrated bioinformatics platform for investigating the human E3 ubiquitin ligase-substrate interaction network. Nature Communications. 2017. 8:347. Link to Springer Nature    57 Citations.
Link to UbiBrowser 1.0     Visits since Apr 24th, 2020
#2021.10.01 UbiBrowser 2.0 was accepted for publication in Nucleic Acids Research (DOI: 10.1093/nar/gkab962).
#2021.09.15 UbiBrowser 2.0 was re-submitted to Nucleic Acids Research.
#2021.08.15 UbiBrowser 2.0 was submitted to Nucleic Acids Research.
#2021.06.01 UbiBrowser 2.0 ESIs/DSIs have been extended to 39 species.
#2018.11.25 UbiBrowser 2.0 was online on Nov 25th, 2018, with DUB-substrate interactions included.
#2017.08.24 UbiBrowser 1.0 was published in Nature Communications.
#2015.07.01 UbiBrowser 1.0 can be used to predict substrates for query E3s.
#2015.04.01 UbiBrowser 1.0 was online on Apr 1st, 2015.
We gratefully acknowledge UbiNet, hUbiquitome and Di Chen et al. iScience:16:177; Oncogene:39:587 for their generously sharing of the ubiquitination datasets.
This work is funded by the:
Program of International S&T Cooperation (2014DFB30020); National Natural Science Foundation of China (31271407, 32088101, 31871341)
Chinese National Key Program of Basic Research (2012CB910300); The National key Research and Development Program of China (2020YFE0202200)
Beijing Talents foundation (to D.L.)