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Database (Oxford). 2017 Jan 1;2017(1). doi: 10.1093/database/bax023.

ABCMdb reloaded: updates on mutations in ATP binding cassette proteins.

Author information

1
MTA-SE Molecular Biophysics Research Group, Hungarian Academy of Sciences and Department of Biophysics and Radiation Biology, Semmelweis University, Budapest 1094, Hungary.
2
Institute of Biochemistry and Molecular Medicine, University of Bern, Bern 3012, Switzerland and.
3
Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest 1117, Hungary.

Abstract

ABC (ATP-Binding Cassette) proteins with altered function are responsible for numerous human diseases. To aid the selection of positions and amino acids for ABC structure/function studies we have generated a database, ABCMdb (Gyimesi et al. , ABCMdb: a database for the comparative analysis of protein mutations in ABC transporters, and a potential framework for a general application. Hum Mutat 2012; 33:1547-1556.), with interactive tools. The database has been populated with mentions of mutations extracted from full text papers, alignments and structural models. In the new version of the database we aimed to collect the effect of mutations from databases including ClinVar. Because of the low number of available data, even in the case of the widely studied disease-causing ABC proteins, we also included the possible effects of mutations based on SNAP2 and PROVEAN predictions. To aid the interpretation of variations in non-coding regions, the database was supplemented with related DNA level information. Our results emphasize the importance of in silico predictions because of the sparse information available on variants and suggest that mutations at analogous positions in homologous ABC proteins have a strong predictive power for the effects of mutations. Our improved ABCMdb advances the design of both experimental studies and meta-analyses in order to understand drug interactions of ABC proteins and the effects of mutations on functional expression.

Database URL:

http://abcm2.hegelab.org.

PMID:
28365738
PMCID:
PMC5467578
DOI:
10.1093/database/bax023
[Indexed for MEDLINE]
Free PMC Article

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