GPCR-OKB Disclaimer

The G Protein Coupled Receptor -
Oligomerization Knowledge Base Project

If checked, GPCR-OKB will search for Oligomers.

Please specify 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.

Example: If you would like to retrieve information about an oligomer of the dopamine D2 receptor, you can either write "dopamine" or "D2".

If you select the "With Phenotypic Changes" option, you will limit your search to only oligomers with demonstrated phenotypic changes.

If you select the "With Proposed Interfaces" option, you can retrieve available information about predicted interfaces of dimerization/oligomerization.

If you select the "With In Vivo Evidence" option, you will limit your search to Oligomers for which at least one of the following 3 criteria are satisfied: 1) Evidence for physical association in native tissue or primary cells; 2) Identification of specific functional property in native tissue; 3) Use of knockout animals or RNAi technology. These criteria are NC-IUPHAR recommendations to recognize a bona fide functional GPCR oligomer, and were reported in detail in Pin J-P, et al., 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.

If you select the "Evidence for Physiological Relevance" option, you will limit your search to Oligomers for which at least two of the following 3 criteria are satisfied: 1) Evidence for physical association in native tissue or primary cells; 2) Identification of specific functional property in native tissue; 3) Use of knockout animals or RNAi technology. These criteria are NC-IUPHAR recommendations to recognize a bona fide functional GPCR oligomer, and were reported in detail in Pin J-P, et al., 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.

Find Oligomers
          With Phenotypic Changes
          With Proposed Interfaces
          With In Vivo Evidence
          With Evidence for Physiological Relevance

If checked, GPCR-OKB will search for Protomers (i.e., constituent subunits of an Oligomer).

Please specify the name of any receptor protomer in the oligomer.

Example: If you would like to retrieve information about dopamine D2 receptor, you can either write "D2" or "dopamine".

Find Protomers

If checked, GPCR-OKB will search for Methods.

Please specify a method type used for the discovery and/or characterization of GPCR oligomers.

Example: If you would like to retrieve information about all oligomers identified by FRET studies, please write "FRET".

Find Methods

Boolean Operators
and	Specifies this term MUST be in the search results - this is the default operator
or	Specifies this term MAY be in the search results
not	Specifies this term MUST-NOT be in the search results

Search Term Modifiers
*	(Wildcard) Can be placed at the front and/or at the end of a search term to find partial term matches
~	(Regular Expression) Can be placed at the front of a search term to search using a regular expression

Special Notes
GPCR-OKB searches are always case-insensitive Any boolean operators provided should be preceding and connected to the term they operate on, for example use +cat not + cat (the extra space between + and cat will not work as desired) GPCR-OKB does not support phrasal or proximity searches

Examples
m1 or m2	Search for items containing the terms m1 or m2
m1 m2	Searches m1 and m2, as "and" is the default search operator
protein not m1 not m2	Search for items with the term protein but not the terms m1 or m2
rotei m2	Search for items which have a term that contains the string 'rotei' and the term m2
adenos* not *a	Search for items which have a term that starts with the string 'adenos' but no terms that end with the string 'a'

Locating Data

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]

References:

Requirements and ontology for a G protein-coupled receptor oligomerization knowledge base. BMC 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, Filizola M.

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

The G Protein Coupled Receptor -Oligomerization Knowledge Base Project

Locating Data

The G Protein Coupled Receptor -
Oligomerization Knowledge Base Project