URL: http://aias.biol.uoa.gr/OMPdb/
Proper Citation: OMPdb (RRID:SCR_006221)
Description: A database of Beta-barrel outer membrane proteins from Gram-negative bacteria. 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 run BLAST searches against the database. The most up-to-date version of the database (as well as all past versions) can be downloaded in various formats (flat text, XML format or raw FASTA sequences). For constructing OMPdb, multiple freely accessible resources were combined and a detailed literature search was performed. The classification of OMPdb''s protein entries into families is based mainly on structural and functional criteria. Information included in the database 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. Along with the database, a collection of profile Hidden Markov Models that were shown to be characteristic for Beta-barrel outer membrane proteins was also compiled. This set, when used in combination with our previously developed algorithms (PRED-TMBB, MCMBB and ConBBPRED) will serve as a powerful tool in matters of discrimination and classification of novel Beta-barrel proteins and whole-genome analyses.
Abbreviations: OMPdb
Synonyms: OMPdb - A database of Beta-barrel outer membrane proteins from Gram-negative bacteria
Resource Type: database, production service resource, data or information resource, service resource, analysis service resource, data analysis service
Defining Citation: PMID:20952406
Keywords: beta-barrel, outer membrane protein, gram-negative bacteria, protein, protein sequence, transmembrane, annotation, genome-wide analyses, comparative genomics, sequence, structure, blast, bio.tools
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University of Athens Biophysics and Bioinformatics Laboratory |
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