OMPdb

OMPdb is a dedicated database that contains beta barrel (β-barrel) outer membrane proteins from Gram-negative bacteria.[1] Such proteins are responsible for a broad range of important functions, like passive nutrient uptake, active transport of large molecules, protein secretion, as well as adhesion to host cells, through which bacteria expose their virulence activity.

OMPdb
Content
Descriptionβ-barrel outer membrane proteins .
OrganismsGram-negative bacteria
Contact
Research centerUniversity of Athens
LaboratoryDepartment of Cell Biology and Biophysics
AuthorsKonstantinos D Tsirigos, Pantelis G. Bagos and Stavros J. Hamodrakas
Primary citationTsirigos & al. (2011)[1]
Release date2011
Access
Websitehttp://www.ompdb.org

Their biological importance together with the inadequate annotation and classification found in public databases, urges the need for intensive studies and accurate data collection regarding β-barrel proteins.

Information included in OMPdb consists of sequence data, as well as annotation for structural characteristics (such as the transmembrane segments), literature references and links to other public databases, features that are unique worldwide. We also offer information regarding the existence of a 3D-structure of a given protein, if it is deposited in the PDB database. A list of protein entries with solved 3D-structure can be also found in each family entry page, when applicable.

Along with the database, a collection of profile Hidden Markov Models, originating mainly from the PFAM[2] database, that were shown to be characteristic for β-barrel outer membrane proteins was also compiled. This set, when used in combination with the recently presented PRED-TMBB2[3] algorithm, will serve as a powerful tool in terms of discrimination and classification of novel β-barrel proteins and whole-proteome analyses.

The web interface of OMPdb offers the user the ability not only to view the available data, but also to submit advanced queries for text search within the database's protein entries or perform protein and domain searches. The most up-to-date version of the database can be downloaded in various formats (flat text, XML format or raw FASTA sequences).

In the download page, the user may download the complete dataset of β-barrel proteins, which is compiled following the regular updates of the PDBTM[4] database, the OPM[5] database and the list of membrane proteins of known 3D-structure from Stephen White's laboratory at UC Irvine.

During 11–12 August 2014, OMPdb participated at the Protein Bioinformatics and Community Resources retreat in the Wellcome Trust Conference Centre, brought together the principal investigators of several specialized protein resources as well as those from protein databases from the large Bioinformatics centres. During this meeting some common key challenges involved in creating and maintaining such resources were discussed, along with various approaches to address them.[6] An important outcome was the creation of a Specialist Protein Resource Network that aims to improve coordination of the activities of its member resources.[7]

References
  1. Tsirigos, Konstantinos D; Bagos Pantelis G; Hamodrakas Stavros J (Jan 2011). "OMPdb: a database of {beta}-barrel outer membrane proteins from Gram-negative bacteria". Nucleic Acids Res. England. 39 (Database issue): D324-31. doi:10.1093/nar/gkq863. PMC 3013764. PMID 20952406.
  2. Finn, Robert D.; Coggill, Penelope; Eberhardt, Ruth Y.; Eddy, Sean R.; Mistry, Jaina; Mitchell, Alex L.; Potter, Simon C.; Punta, Marco; Qureshi, Matloob (2016-01-04). "The Pfam protein families database: towards a more sustainable future". Nucleic Acids Research. 44 (D1): D279–285. doi:10.1093/nar/gkv1344. ISSN 1362-4962. PMC 4702930. PMID 26673716.
  3. Tsirigos, Konstantinos D.; Elofsson, Arne; Bagos, Pantelis G. (2016-09-01). "PRED-TMBB2: improved topology prediction and detection of beta-barrel outer membrane proteins". Bioinformatics. 32 (17): i665–i671. doi:10.1093/bioinformatics/btw444. ISSN 1367-4811. PMID 27587687.
  4. Kozma, Dániel; Simon, István; Tusnády, Gábor E. (2013-01-01). "PDBTM: Protein Data Bank of transmembrane proteins after 8 years". Nucleic Acids Research. 41 (Database issue): D524–529. doi:10.1093/nar/gks1169. ISSN 1362-4962. PMC 3531219. PMID 23203988.
  5. Lomize, Mikhail A.; Pogozheva, Irina D.; Joo, Hyeon; Mosberg, Henry I.; Lomize, Andrei L. (2012-01-01). "OPM database and PPM web server: resources for positioning of proteins in membranes". Nucleic Acids Research. 40 (Database issue): D370–376. doi:10.1093/nar/gkr703. ISSN 1362-4962. PMC 3245162. PMID 21890895.
  6. Holliday, Gemma L.; Bairoch, Amos; Bagos, Pantelis G.; Chatonnet, Arnaud; Craik, David J.; Finn, Robert D.; Henrissat, Bernard; Landsman, David; Manning, Gerard (2015-06-01). "Key challenges for the creation and maintenance of specialist protein resources". Proteins. 83 (6): 1005–1013. doi:10.1002/prot.24803. ISSN 1097-0134. PMC 4446195. PMID 25820941.
  7. Babbitt, Patricia C.; Bagos, Pantelis G.; Bairoch, Amos; Bateman, Alex; Chatonnet, Arnaud; Chen, Mark Jinan; Craik, David J.; Finn, Robert D.; Gloriam, David (2015-01-01). "Creating a specialist protein resource network: a meeting report for the protein bioinformatics and community resources retreat". Database: The Journal of Biological Databases and Curation. 2015: bav063. doi:10.1093/database/bav063. ISSN 1758-0463. PMC 4499208. PMID 26284514.


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