ABCM2 - ABCMdb reloaded - a central knowledgebase for variations in ABC genes
The ABC mutations database contains mentions of ABC protein mutations extracted from the literature using automated data mining method and also annotated infromation on variants from other databases and sources.
|Our database is a member of
The Human Variome Project.
|ABCMdb is referenced in the UniProt database in the
'Web resources' section (an example).
- Mutations are identified automatically and stored in the database
After mutation extraction, the hits for ABCC6, G1, G2, G5 and G8 were verified manually to assure data quality, constituting a benchmark set. There is also an on-line manual curation function, so that registered users can mark individual mentions of mutations as correct or incorrect. The database is updated with recent PubMed search hits once a year.
- Alignments for comparative analysis of mutations
The web application make it easy to look up mutations in and around homologous positions in various other ABC proteins (Browse – select protein – list all mutations – select mutation – homologous mutations). Alignments are provided for certain regions of ABC proteins, but custom alignments can also be uploaded (MyProfile – alignments).
- Mapping the mutations in 3D
The web applications also allows the mapping of amino acid positions onto 3D models of proteins or domains with the map mutations function (Browse – select protein – map mutations). Homologous positions are calculated using alignments. Custom PDB files with protein structures can also be uploaded (MyProfile – PDB files).
- Predicted effect of mutations are inserted
Because of the low number of available data on the effect of variations, even in the case of the widely studied disease causing ABC proteins, we inserted the possible effects of mutations predicted by SNAP2 and PROVEAN.
- The database is supplemented with information at the DNA level
We inserted information on the whole ABC genes to be able to query, find, and interpret the effect of mutations in non-coding regions. We also aim to include not only introns, but also regulatory informations such as transcription binding sites.
If you find our database useful, please cite:
Gyimesi G, Borsodi D, Sarankó H, Tordai H, Sarkadi B, Hegedűs T.
"ABCMdb: A database for the comparative analysis of protein mutations in ABC transporters, and a potential framework for a general application."
Hum Mutat. 2012 Nov;33(11):1547-56. PMID: 22693078