Computational resources for ubiquitin and ubiquitin-like conjugation:

<1> Public Databases

<2> Computational Algorithms and Tools

  (1) Ubiquitination

  (2) Ubiquitin-like modification

last updated: Sep, 2016

<1> Public Databases:

1. UbiProt: a new resouce of ubiquitinated proteins comprising information about protein properties and sources maintained by Ubiquitin Research Group at Central Research Laboratory of Nizhny Novgorod State Medical Academy (Russia) (Chernorudskiy, et al., 2007).

2. SCUD: a database of ubiquitin conjugation system in Saccharomyces cerevisiae, including E1s, E2s, E3s, substrates and deubiquitination enzymes (Lee, et al., 2008).

3. plantsUPS: a genomics database of ubiquitin conjugation system in plants including Arabidopsis, Rice, Poplar, Soybean, Grape, Medicago and Maize (Zhou, et al., 2009).

4. PlantsUBQ: a database of ubiquitin proteasome pathway in palnts and a project to describe the network of Arabidopsis ubiquitination proteins Funded by the National Science Foundation 2010 Program (USA).

5. hUbiquitome: a database of human ubiquitin conjugation proteins and ubiquitin binding-site sequences (Du, et al., 2011).

6. E3NET: a system of E3-substrate networks and a systematic framework to analyze E3-mediated regulatory networks in various cellular functions (Han, et al., 2012).

7. PupDB: a database of proteins with Prokaryotic ubiquitin-like protein(Pup) modification. It displays the structures of pupylated proteins and pupylation sites (Tung, et al., 2012).

8. UUCD 1.0: a comprehensive database of ubiquitin and ubiquitin-like conjugation contains E1s, E2s, E3s and DUBs from 70 eukaryotic species (Gao, et al., 2013).

9. DUDE-db: a database of ubiquitin (UB) and deubiquitinating (DUB) enzymes across multiple eukaryotic genomes (Hutchins AP, et al., 2013).

10. Human E3 Ubiquitin Ligases: a comprehensive database of human E3 ubiquitin ligases (Medvar B, et al., 2016).

<2> Computational Algorithms and Tools

 (1) Ubiquitination:

1. Methods for the functional genomic analysis of ubiquitin ligases (Li, et al., 2005). The tool is not available.

2. Prediction of ubiquitin proteins using artificial neural networks, hidden Markov model and support vector machines. (Jaiswal, et al., 2007). The tool is not available.

3. UbiPred: a predictor to predict potential ubiquitination sites (Tung, et al., 2008).

4. E3Miner: a text mining tool to extract comprehensive knowledge of ubiquitin-protein ligases from available articles and databases (Lee, et al., 2008).

5. UbPred: a random forest predictor to identify potential ubiquitination sites from ubiquitinated substrates (Radivojac, et al., 2010).

6. CKSAAP_UbSite: a tool to predict ubiquitination sites from ubiquitinated protein sequences (Chen, et al., 2011).

7. Prediction of lysine ubiquitination with mRMR feature selection and analysis (Cai, et al., 2011). The tool is not available.

8. GPS-ARM: a novel software to predict D-boxes and KEN-boxes of APC/C-mediated substrates (Liu, et al., 2012).

9. WPNNA: a weighted passive nearest neighbor algorithm to predict ubiquitination sites (Feng, et al., 2012). The tool is not available.

10. Prediction of lysine ubiquitylation with ensemble classifier and feature selection (Zhao, et al., 2012). The tool is not available.

 (2) Ubiquitin-like modification:

1. SUMOsp 1.0: the old version of SUMOsp program for sumoylation site prediction (Xue, et al., 2006).

2. SUMOsp 2.0: a new SUMOsp program to specifically predict sumoylation sites in sumoylatd proteins. (Ren, et al., 2009).

3. Predicting sumoylation site by feature selection method. (Cai, et al., 2011). The tool is not available.

4. GPS-PUP: a predictor to predict pupylation sites in prokaryotic proteins. (Liu, et al., 2011).