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Bio <-> Chem

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

Update,  13 March,  most pleased to see this today and thanks for the acesses ************************************************************* This starts where I tried out some InChiKey (IK)  searching  for the bosinhib blog post in June of last year. Soon after I was pleased to have a proposal accepted  for the InChI special issue. I am also a supporting member of the InChI Trust (which you can also join).

ChemChemicalize.orgPubChemBiologieAnglais
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Auteur Christopher Southan

For those of you new to chemicalize.org it is a unique open application that recognizes different types of chemical names in text sources and converts them into structures. It can thus disinter many millions of these from their document toombs.  It not only features in some of my own posts but there is also a ChemAxon UGM video, from yours truly, and  the resource has its has its own blog.

AntimalarialsBioDrug TargetMechanism Of ActionBiologieAnglais
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Auteur Christopher Southan

Update:  Sequel post antimalarial-target-deconvolution-part II To deconvolute , or not , that is the question: Whether 'tis Nobler in the mind to suffer The Slings and Arrows of outrageous target-centricity Or to take up phenotypic screening  against a Sea of unvalidated targets ?

ChemPatentsPubChemSureChemBiologieAnglais
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Auteur Christopher Southan

The by-line for this post could be "from famine to feast" but context is available from the SureChem press release (SC), the SureChem blog  and a PubChem news flash (PC).  I also wrote a short piece on the prescient Nature News announcement back in April (including some speculative CAS substances: CID factoring).   More technical background can be found in previous posts on PubChem-pips-9-million-patent-structures

BioMRCNCATSRepurposingBiologieAnglais
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Auteur Christopher Southan

Updates, 11 Jan 2013, a) an orthogonal backstory from one of my esteemed co-authors  b) I am pleased to be involved in the planning of a repurposing workshop at BioIT 2013, April, in Boston. One of the benefits of blogging is to be able to add extra bits of context to your own papers,  in this case  "Challenges and recommendations for obtaining chemical structures of industry-provided repurposing candidates"

BioChemicalize.orgMalariaOSDDBiologieAnglais
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Auteur Christopher Southan

Update: 30th Nov.  The latest G+ posts  indicate data from the Sydney team are now being piped direct to ChEMBL so I'll take a look when it surfaces.   This recent slide set  from SE had a particularly pertinent diagram so I have added this below.   This piece was inspired by conjunctions related to recent  G+ posting, from an OSDD Malaria Team Leader (see comment) and

AZD5904BioMyloperoxidaseBiologieAnglais
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Auteur Christopher Southan

I’m more interested in visitor milestones (and thanks to everyone for pushing these towards 15K and ~1.7K pm) rather than posting metrics, but I thought the 50th post warranted a little extra.  As if by magic, something popped up in my Twitter feed a few days ago which spawned a set of connectivities that intersected with a number of themes I have been engaging with, both here and in recent manuscripts.

ChemPatentsSKL-NPBiologieAnglais
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Auteur Christopher Southan

The Korean medicinal chemists that feature in the In The Pipeline “Oops we didn’t mean to publish that” posting could be forgiven for feeling a little hapless in the face of this exposure of the interesting results published in their paper and patents.