ABCMdb: a database for the comparative analysis of protein mutations in ABC transporters, and a potential framework for a general application.
To overcome the pathological phenomena caused by altered function of ABC (ATP Binding Cassette) proteins, their mechanisms of action are extensively investigated, often involving the design of mutant constructs for experiments. Designing mutagenetic constructs, interpreting the result of mutagenetic experiments, and finding individual genetic variants require an extensive knowledge of previously published mutations. To aid the recapitulation of mutations described in the literature, we set up a database of ABC protein mutations (ABCMdb) extracted from full-text papers using an automatic mining approach. We have also developed a Web application interface to compare mutations in different ABC proteins using sequence alignments and to interactively map the mutations to 3D structural models. Currently our database contains protein mutations published for ABCB1, ABCB11, ABCC1, ABCC6, ABCC7, and the proteins of the ABCG subfamily. The database will be extended to include other members and subfamilies, and to provide information on whether or not a mutation is disease causing, represents a high-incidence polymorphism, or was generated only in vitro. The ABCMdb database should already help to compare the effects of mutations at homologous positions in different ABC proteins, and its interactive tools aim to advance the design of experiments for a wider range of proteins.
Membrane Research Group, Hungarian Academy of Sciences, Budapest, Hungary.
Gergely
G
Gyimesi
Dávid
D
Borsodi
Hajnalka
H
Sarankó
Hedvig
H
Tordai
Balázs
B
Sarkadi
Tamás
T
Hegedűs
D018528:ATP-Binding Cassette Transporters / Q000737:chemistry / Q000235:genetics*; D057225:Data Mining; D030562:Databases, Protein / Q000706:statistics & numerical data; D006801:Humans; D020407:Internet; D008958:Models, Molecular; D009154:Mutation; D011487:Protein Conformation; D039781:PubMed; D016415:Sequence Alignment; D012984:Software; D040681:Structural Homology, Protein; D014584:User-Computer Interface
D018528:ATP-Binding Cassette Transporters