What is it about?
G protein–coupled receptors (GPCRs) are a large protein family of receptors that sense molecules interacting with the cell surface which then activate important signal pathways in the cytoplasm (https://en.wikipedia.org/wiki/G_protein%E2%80%93coupled_receptor). They also form one of the major drug target classes for established human medicines and the development of new ones. Because this importance has lead to 1000's of publications those interested in GPCRs can find it difficult to select and retrieve concise information. Databases go a long way towards solving this problem because they are an excellent source of collated facts and reference sequences distilled from decades of scholarly literature. However, even choosing between the many different databases is not straightforward, whether they are general (i.e. covering all proteins) or GPCR-focussed. This short article selects a limited number of databases as a "core set" that will be useful for students and researchers.
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Why is it important?
As we know, GPCRs have always been important for biochemistry and pharmacology and, as a target class for drug discovery research, this is now being boosted by a steady stream of solved structures over the last few years, including the definition of ligand binding sites. However, as the number of possibly relevant databases pushes above 40 (Kowalsman et al 2014, referenced in the article) GPCR researchers may suffer from "paralysis of choice" (a.k.a. too much of a good thing). This article aims to at least partially ameliorate the paralysis via a recommended short list of just 14 sources, including two first-stop entry portals. Most of these databases have published detailed update papers within the last two years and they all have a declared update frequency. It is hoped this article is timely in complementing the other articles in the special issue on New Technologies for GPCRs.
Perspectives
While short articles are challenging to write, I was aided in this case by very useful iterations with the special issues Editors who thus take some credit for the final structure. My introduction of primary-secondary-tertiary classification was slightly contentious but I hope readers will find useful. Resource utility judgments and choices are always difficult, even (or perhaps especially) for those with some cognisance of the database ecosystem (and working for one in my case). I thus decided early on to be parsimonious in what I should include. For sure the list may be biased but it was supported by recent publications, declared update frequencies (although I was not always able to independently verify these had actually happened). I also weighed up what can be called "reputational persistence". Since ClinVar and SureChEMBL are relatively new compared to the others, this does not apply but they do seem to be well resourced. I should finish by adding that while inclusion of any resource was an explicitly positive judgment on my part, the converse is not the case (i.e. omitted resources should not take this as a negative judgment)
Dr Christopher Southan
Read the Original
This page is a summary of: Retrieving GPCR data from public databases, Current Opinion in Pharmacology, October 2016, Elsevier,
DOI: 10.1016/j.coph.2016.07.002.
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