BiologiaIngleseBlogger

Bio <-> Chem

Technical notes from the interface between bioinformatics and cheminformatics by Chris Southan
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BiologiaInglese
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Autore Christopher Southan

As readers of this blog may be aware, related to my long-standing involvement with the Sydney-based Open Source Malaria (OSM) team,  I occasionally post what I hope are useful PubChem mappings for antimalarial compounds extracted either from review articles or research papers (search "antimalarial on this blog").  More recently, since 2017,  the GtoPdb

ChEMBLGtoPdbPubChemBiologiaInglese
Pubblicato
Autore Christopher Southan

Update: 10 Feb 2019 see these new ELIXIR Core Data Resource Profiles for more context.  Five of these feature in this post. Update 12 Nov 2018, Its good to see a new NAR paper describing BRENDA in detail (PMID 30395242). Particularly notable is

BiologiaInglese
Pubblicato
Autore Christopher Southan

Below is a slide from our BACE1 entry that I presented in my hemi-annual "state of the proteases" (in our database) update at our IUPHAR/GtoPdb meeting in Edinburgh, 19-20th May 2018. This post touches on the technicalities of what is included,  what is missing and what is planned to get in for the next release (i.e. the  page above will refresh ~ end of June).

AntimalarialsBiologiaInglese
Pubblicato
Autore Christopher Southan

The 2018 World Malaria Day was on Wednesday the 25th of April.  Since I have been a volunteer for the Sydney-based Open Source Malaria project since 2012  I am pleased to be included in their own announcement page that reverberated around Twitter and got into LinkedIN also on that day.

BiologiaInglese
Pubblicato
Autore Christopher Southan

For my sins, but possibly some virtues also,  I have recently been appointed to the SAB of Phyre (Protein Homology/analogY Recognition Engine). As has been already explored by the team (e.g. PhyreStorm, BackPhyre, PhyreRisk) the punning possibilities are endless... .

BiologiaInglese
Pubblicato
Autore Christopher Southan

The context of this post arises out of a recent SAFER consortium kick-off meeting.  This slide (19)  from my presentation introduces the compound in question "3b" in PMID 28943244 from an Italian/Polish research team. Noting the outstanding 5-HT2A receptor affinity and selectivity of compound 3b (Ki = 0.0224 nM)  and possible utility for SAFER, this is has now been curated in our latest release as

BiologiaInglese
Pubblicato
Autore Christopher Southan

Bad news, as per below. After some pitching in over on twitter this had two unexpected consequences.  Firstly,  I got phoned by a journalist for 5 minutes of fame in Nature news (2nd time now..). Secondly it turns out my 117 comments over five years had got me into the top-ten no less.  So what to do?  I cant devote a lot of time to such archiving so

AntimalarialsBiologiaInglese
Pubblicato
Autore Christopher Southan

Update: 6th Oct - two comments below post (on LinkedIN and G+ also) plus a couple of tweets/replies.  *********************************** The initial chemical structure findability results for our paper " Open Source Drug Discovery: Highly Potent Antimalarial Compounds Derived from the Tres Cantos Arylpyrroles " (PMID 27800551) from a year ago, were blogged about here.

PubChemBiologiaInglese
Pubblicato
Autore Christopher Southan

Update 19th Nov Nature have just instigated an initiative to enhance chemical structure drawing.  In the form of a ChemDraw style sheet this is expected to lead to less intervention by production editors for Nature Chemistry, Nature Chemical Biology, Nature Nanotechnology, etc (sic) Nature Communications and Nature Reviews Chemistry, Nature Reviews Materials, etc. (sic, including NR Drug Discovery?).

GPCR. LigandsBiologiaInglese
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Autore Christopher Southan

Its not every day an orphan GPCR becomes de-orphanized.  Its even rarer that the ligand looks like a "new" cytokine and even rarer still that two independent papers cross-corroborate essentially the same findings in the same week.  Yet more exceptionality in this case is that the pairing becomes immediately relevant to our GtoImmuPdb effort.