Dataset Information

GPCR-OKB: the G Protein Coupled Receptor Oligomer Knowledge Base.

ABSTRACT:

Summary

Rapid expansion of available data about G Protein Coupled Receptor (GPCR) dimers/oligomers over the past few years requires an effective system to organize this information electronically. Based on an ontology derived from a community dialog involving colleagues using experimental and computational methodologies, we developed the GPCR-Oligomerization Knowledge Base (GPCR-OKB). GPCR-OKB is a system that supports browsing and searching for GPCR oligomer data. Such data were manually derived from the literature. While focused on GPCR oligomers, GPCR-OKB is seamlessly connected to GPCRDB, facilitating the correlation of information about GPCR protomers and oligomers.

Availability and implementation

The GPCR-OKB web application is freely available at http://www.gpcr-okb.org

SUBMITTER: Khelashvili G

PROVIDER: S-EPMC2894509 | biostudies-literature | 2010 Jul

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

GPCR-OKB: the G Protein Coupled Receptor Oligomer Knowledge Base.

Khelashvili George G Dorff Kevin K Shan Jufang J Camacho-Artacho Marta M Skrabanek Lucy L Vroling Bas B Bouvier Michel M Devi Lakshmi A LA George Susan R SR Javitch Jonathan A JA Lohse Martin J MJ Milligan Graeme G Neubig Richard R RR Palczewski Krzysztof K Parmentier Marc M Pin Jean-Philippe JP Vriend Gerrit G Campagne Fabien F Filizola Marta M

Bioinformatics (Oxford, England) 20100525 14

<h4>Summary</h4>Rapid expansion of available data about G Protein Coupled Receptor (GPCR) dimers/oligomers over the past few years requires an effective system to organize this information electronically. Based on an ontology derived from a community dialog involving colleagues using experimental and computational methodologies, we developed the GPCR-Oligomerization Knowledge Base (GPCR-OKB). GPCR-OKB is a system that supports browsing and searching for GPCR oligomer data. Such data were manuall ...[more]

PMID: 20501551

Similar Datasets

Project description:BACKGROUND: G protein-coupled receptors (GPCRs) transduce a wide variety of extracellular signals to within the cell and therefore have a key role in regulating cell activity and physiological function. GPCR malfunction is responsible for a wide range of diseases including cancer, diabetes and hyperthyroidism and a large proportion of drugs on the market target these receptors. The three dimensional structure of GPCRs is important for elucidating the molecular mechanisms underlying these diseases and for performing structure-based drug design. Although structural data are restricted to only a handful of GPCRs, homology models can be used as a proxy for those receptors not having crystal structures. However, many researchers working on GPCRs are not experienced homology modellers and are therefore unable to benefit from the information that can be gleaned from such three-dimensional models. Here, we present a comprehensive database called the GPCR-SSFE, which provides initial homology models of the transmembrane helices for a large variety of family A GPCRs. DESCRIPTION: Extending on our previous theoretical work, we have developed an automated pipeline for GPCR homology modelling and applied it to a large set of family A GPCR sequences. Our pipeline is a fragment-based approach that exploits available family A crystal structures. The GPCR-SSFE database stores the template predictions, sequence alignments, identified sequence and structure motifs and homology models for 5025 family A GPCRs. Users are able to browse the GPCR dataset according to their pharmacological classification or search for results using a UniProt entry name. It is also possible for a user to submit a GPCR sequence that is not contained in the database for analysis and homology model building. The models can be viewed using a Jmol applet and are also available for download along with the alignments. CONCLUSIONS: The data provided by GPCR-SSFE are useful for investigating general and detailed sequence-structure-function relationships of GPCRs, performing structure-based drug design and for better understanding the molecular mechanisms underlying disease-associated mutations in GPCRs. The effectiveness of our multiple template and fragment approach is demonstrated by the accuracy of our predicted homology models compared to recently published crystal structures.

Dataset Information

GPCR-OKB: the G Protein Coupled Receptor Oligomer Knowledge Base.

Summary

Availability and implementation

Publications

GPCR-OKB: the G Protein Coupled Receptor Oligomer Knowledge Base.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets