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...

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Bibliographic Details
Published in:Human mutation 2012-11, Vol.33 (11), p.1547-1556
Main Authors: Gyimesi, Gergely, Borsodi, Dávid, Sarankó, Hajnalka, Tordai, Hedvig, Sarkadi, Balázs, Hegedűs, Tamás
Format: Article
Language:English
Subjects:
ABC proteins
ATP-Binding Cassette Transporters - chemistry
ATP-Binding Cassette Transporters - genetics
Data Mining
Databases, Protein - statistics & numerical data
Humans
Internet
Models, Molecular
Mutation
Protein Conformation
protein mutations
PubMed
Sequence Alignment
Software
Structural Homology, Protein
text mining
User-Computer Interface
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Summary: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. Hum Mutat 33:1547–1556, 2012. © 2012 Wiley Periodicals, Inc.
ISSN:1059-7794
1098-1004
DOI:10.1002/humu.22138