ArticleNucleic acids research2011
OMPdb: a database of {beta}-barrel outer membrane proteins from Gram-negative bacteria.
Article in Nucleic acids research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed, 67 citations in OpenAlex.
- MetaMP Ecosystem for Unified, Auditable, and Benchmark-Ready Data for Reliable Membrane Protein Annotation.Computational and structural biotechnology journal · 2026Article
- The Name Is Barrel, β-Barrel.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Protein-lipid charge interactions control the folding of outer membrane proteins into asymmetric membranes.Nature chemistry · 2023Article
- General features of transmembrane beta barrels from a large database.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Analysis of bacterial pangenomes reduces CRISPR dark matter and reveals strong association between membranome and CRISPR-Cas systems.Science advances · 2023Article
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- A Novel Design of Multi-epitope Vaccine AgainstInternational journal of peptide research and therapeutics · 2021Article
- Computational prediction of secreted proteins in gram-negative bacteria.Computational and structural biotechnology journal · 2021Review
- OMPdb: A Global Hub of Beta-Barrel Outer Membrane Proteins.Frontiers in bioinformatics · 2021Article
- Hidden neural networks for transmembrane protein topology prediction.Computational and structural biotechnology journal · 2021Article
- Guardians of the Cell: State-of-the-Art of Membrane Proteins from a Computational Point-of-View.Methods in molecular biology (Clifton, N.J.) · 2021Article
- The Role of SurA PPIase Domains in Preventing Aggregation of the Outer-Membrane Proteins tOmpA and OmpT.Journal of molecular biology · 2019Article
- Braun's Lipoprotein Facilitates OmpA Interaction with the Escherichia coli Cell Wall.Biophysical journal · 2017Article
- In Silico Structure and Sequence Analysis of Bacterial Porins and Specific Diffusion Channels for Hydrophilic Molecules: Conservation, Multimericity and Multifunctionality.International journal of molecular sciences · 2016Article
- Properties and Phylogeny of 76 Families of Bacterial and Eukaryotic Organellar Outer Membrane Pore-Forming Proteins.PloS one · 2016Article
- Divergence between the Highly Virulent Zoonotic Pathogen Helicobacter heilmannii and Its Closest Relative, the Low-Virulence "Helicobacter ailurogastricus" sp. nov.Infection and immunity · 2016Article
- Molecular Simulations of Gram-Negative Bacterial Membranes: A Vignette of Some Recent Successes.Biophysical journal · 2015Review
- Databases for Microbiologists.Journal of bacteriology · 2015Review
- Prediction of structural features and application to outer membrane protein identification.Scientific reports · 2015Article
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We describe here OMPdb, which is currently the most complete and comprehensive collection of integral β-barrel outer membrane proteins from Gram-negative bacteria. The database currently contains 69,354 proteins, which are classified into 85 families, based mainly on structural and functional criteria. Although OMPdb follows the annotation scheme of Pfam, many of the families included in the database were not previously described or annotated in other publicly available databases. There are also cross-references to other databases, references to the literature and annotation for sequence features, like transmembrane segments and signal peptides. Furthermore, via the web interface, the user can not only browse the available data, but submit advanced text searches and run BLAST queries against the database protein sequences or domain searches against the collection of profile Hidden Markov Models that represent each family's domain organization as well. The database is freely accessible for academic users at http://bioinformatics.biol.uoa.gr/OMPdb and we expect it to be useful for genome-wide analyses, comparative genomics as well as for providing training and test sets for predictive algorithms regarding transmembrane β-barrels.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.