The information contained in GPCR-OKB can be accessed either by browsing or searching through any of the following concepts or combination of them: Oligomers, Protomers, Methods, Phenotypic Changes, and/or Physiological Relevance. To get to the Browse page, click the "Browse" link in the navigation menu. To Search for concepts or combinations of them, please refer to the Search engine at the top right side of the page. The default search type is "Oligomer". The icons on the search and result pages will tell you more about what the different options mean and how to use them. More details about the search options follow.
- Searching by Oligomer Name
You can search the information contained in GPCR-OKB by specifying the name of the oligomer of interest made up of the names of the protomers that form its constituent parts. "The "Oligomer" option is checked by default. If you select the "With Phenotypic Changes", "With Proposed Interfaces", "With In Vivo Evidence", or "With Evidence for Physiological Relevance" options in the oligomer search field, you will limit your search to only oligomers with demonstrated phenotypic changes, proposed interfaces, in vivo evidence, or evidence for physiological relevance, respectively.
- Searching by Protomer Name
You can search the information contained in GPCR-OKB by specifying the name of the constituent subunits of the oligomer, and checking the "Protomer" option.
- Searching by Method Type
You can search the information contained in GPCR-OKB by specifying the computational or experimental procedures used to characterize the oligomer, e.g., Fluorescence Resonance Energy Transfer (FRET), Bioluminescence Resonance Energy Transfer (BRET), Time Resolved FRET (TR-FRET), cross-linking, co-immunoprecipitation, Atomic Force Microscopy (AFM), correlated mutation analysis, etc.
- Searching by Phenotypic Change
You can search the information contained in GPCR-OKB by looking for phenotypic changes recorded with specific ligands relative to any of the component protomers, e.g., specific signaling, ligand recognition, etc. A change occurs if the phenotype of the oligomer is significantly different from the phenotype of any of its constituent protomers.
- Searching by In Vivo Evidence
You can search the information contained in GPCR-OKB by looking for in vivo evidence, e.g., colocalization in native tissues, in vivo effects of oligomer specific ligands, in vivo phenotypic changes (e.g., pharmacological response or cooperativity) in knock-out animals, etc.
- Searching by Evidence for Physiological Relevance
You can search the information contained in GPCR-OKB by looking for adherence to at least two NC-IUPHAR criteria concerning proof of existence in vivo [Pin J-P, Neubig R, Bouvier M, Devi L, Filizola M, Javitch JA, Lohse MJ, Milligan G, Palczewski K, Parmentier M, Spedding M: International Union of Basic and Clinical Pharmacology. LXVII. Recommendations for the Recognition and Nomenclature of G Protein-Coupled Receptor Heteromultimers. Pharmacological Reviews 2007, 59(1):1-9]
Requirements and ontology for a G protein-coupled receptor oligomerization
Bioinformatics. 2007 May 30;8:177. Skrabanek L,
Murcia M, Bouvier M, Devi L, George SR, Lohse MJ, Milligan G, Neubig R,
Palczewski K, Parmentier M, Pin JP, Vriend G, Javitch JA, Campagne F,
GPCR-OKB: The G Protein Coupled Receptor Oligomer Knowledge Base.
Bioinformatics. 2010 May 25.
Khelashvili G, Dorff K, Shan J, Camacho-Artacho M, Skrabanek L, Vroling B, Bouvier M, Devi LA, George SR,
Javitch JA, Lohse MJ, Milligan G, Neubig RR, Palczewski K, Parmentier M, Pin JP, Vriend G, Campagne F,
Filizola M. doi:10.1093/bioinformatics/btq264