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Updated: Jun 8, 2026

From Constructs to Crystals – Towards Structure Determination of β-barrel Outer Membrane Proteins
Published on: July 4, 2016
OMPdb: a database of {beta}-barrel outer membrane proteins from Gram-negative bacteria
Konstantinos D Tsirigos1, Pantelis G Bagos, Stavros J Hamodrakas
1Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Athens 15701, Greece.
OMPdb is a comprehensive database of integral beta-barrel outer membrane proteins from Gram-negative bacteria, offering extensive data for genomic and predictive analyses.
Area of Science:
- Biochemistry
- Bioinformatics
- Genomics
Background:
- Integral beta-barrel outer membrane proteins are crucial components of Gram-negative bacteria.
- Existing databases lack comprehensive collections of these proteins.
Purpose of the Study:
- To present OMPdb, the most complete database of integral beta-barrel outer membrane proteins.
- To provide a resource for genome-wide analyses and predictive algorithm development.
Main Methods:
- Database compilation of 69,354 proteins from Gram-negative bacteria.
- Classification into 85 families based on structural and functional criteria.
- Inclusion of cross-references, literature links, and sequence feature annotations.
Main Results:
- OMPdb contains 69,354 integral beta-barrel outer membrane proteins classified into 85 families.
- Many families are novel and not found in other databases.
- Includes annotations for transmembrane segments and signal peptides.
Conclusions:
- OMPdb is a valuable, freely accessible resource for researchers.
- Facilitates comparative genomics and the development of predictive models for transmembrane beta-barrels.
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