UbiNet is a knowledge-based system that could provide potential E3 ligases for ubiquitinated proteins by the information of protein-protein interactions and substrate site specificities. The UbiNet could help users to identify E3 ligase-mediated ubiquitination networks and their roles in biological processes. The current databases of UbiNet contains 499 experimentally verified E3 ligases, 14692 ubiquitinated substrate proteins, 430530 data of protein-protein interaction, and 2143 data of E3-associated functional categories.
To reconstruct the networks, users just follows the steps as suggested by the pages :
| 1. | Input a list of genes (containing E3 ligases, ubiquitinated substrate proteins, or interacting proteins). |
| 2. | Select the organism (At the current version of UbiNet 1.0; only human organism is provided!). |
| 3. | Submit. |
If the query list contains only E3s, our system will visualize networks of these E3s with all possible ubiquitinated substrate proteins. Otherwise, our system will show networks between E3s ligases, ubiqtuinated substrate proteins, and interacting protein in the given list. Two case studies (Case Study 1; Case Study 2) are provided at the bottom of the pages, users can quickly seek and investigate the regulatory networks through these two case studies.