Version 2.0 released January 30th 2007

The aim of the resource is to gather together information related to ubiquitination and related pathways. The initial version of the resource focuses on the E2, ubiquitin and ubiquitin-like protein conjugating enzymes (UBCs), containing a sequence alignment of the E2 family, a phylogenetic tree, homology models, and a comparison of their electrostatic potentials. In addition there is a list of all the ubiquitin related structures that we have found in the pdb.

The current E2 models and electrostatic potentials served from the main page are the result of one modelling event. There are 1649 of these. We have developed an automated pipeline that models new E2 sequences as they are released, and calculate their electrostatic potentials. As of writing (28th Jan 2007) the pipeline is being tested. Approximately 700 structures need to be modelled to keep the site actual with the current UBC entries in the SMART database. After this the site will be kept actual with SMART. We also intend to extend the website to cover wider aspects of ubiquitination. Currently we have no code integrated to deal with synonymous entries, which means that some queries will produce synonyms in the output. The plus side of this is that the user will have an indication of the consistency of the modelling and comparison process, however synonyms in the results will be removed at sometime in the future.

Contents and Further description.

The site is a result of a collaboration between the groups of Dr Amit Banerjee at Wayne State University, Detroit and Dr Rebecca Wade at EML Research and EMBL, Heidelberg. This work has been supported by National Institutes of Health (USPHS) grant GM59467 and the Klaus Tschira Foundation.