• Antibody Drugs in Development


    There are a large number of antibody drugs in development - there are about 580 in the current ChEMBL list (click here for Excel spreadsheet). I've stripped out some of the fields for clarity, but it should be pretty obvious what everything is.

    So, given that we'll start loading our biological drug sets into ChEMBL shortly, is there any key data missing, as always, any feedback on errors, etc would be greatly appreciated. If anyone would like a file of all the sequences that we have, let me know.

    A couple of notes on the data content

    • There will be some duplication - due primarily to the INNs not being released with Research Code information, whereas from clinicaltrials.gov they typical enter via a Research Code name - after a few months the entries are linked. So any further information on this set would be greatly appreciated....
    • The Phase number refers to the highest phase I could find the antibody drug reaching in the broad literature - it does not capture current status, and in fact a large number of these will have been abandoned by now.
    • There are some ambiguities (to me at least) over the USAN year, I use the date the name is published, USAN themselves appear to use a sometimes backdated date, this is probably due to inevitable gaps between assignment of the name and it's publication.

  • Another paper about ChEMBL


    A paper on ChEMBL has just been published in Nucleic Acids Review Database Issue. If NAR is new to you, it is the de facto place for publishing new (and updates to) online biological data sources.

    A link to the advance access free, Open Access paper is here.


    %T ChEMBL: a large-scale bioactivity database for drug discovery
%A A Gaulton
%A LJ Bellis
%A AP Bento
%A J Chambers
%A M Davies
%A A Hersey
%A Y Light 
%A S McGlinchey
%A D Michalovich
%A B Al-Lazikani 
%A JP Overington
%J Nucleic Acids Research
%D 2011 
%O doi:10.1093/nar/gkr777

  • A paper about ChEMBL


    There is a new paper on ChEMBL just published in Biochem. Soc. Trans. The paper itself is here (subscription required). 

    %T Collation and data-mining of literature bioactivity data for drug discovery
%A LJ Bellis
%A R Akhtar
%A B Al-Lazikani
%A F Atkinson
%A AP Bento 
%A J Chambers
%A M Davies
%A A Gaulton
%A A Hersey
%A K Ikeda
%A FA Krueger
%A Y Light
%A S McGlinchey
%A R Santos
%A B Stauch
%A JP Overington
%J Biochem. Soc. Trans
%V 39
%P 1365-1370
%D 2011

  • Gone Fishin'


    Things will be fairly quiet for the next week at ChEMBL Manor - we're off on our annual research retreat - this time to Kent. So please allow us a little more time to get back to emails, etc.

  • Protein Descriptors


    Some time ago we asked about protein descriptor services on the web - the long and short of it is that, there really wasn't anything that fit our needs, so we wrote one. Given a sequence it returns a long vector of descriptors, things like hydrophobicity, fraction of each amino acid, pI, and a whole bunch of other stuff. If there is interest, we could open this up as a web service - so return a JSON or XML object in real time (and for UniProt sequences have these precalculated). There will be some licensing issues for some of the descriptors, but I'm sure we can sort something out.

  • International Chemical Biology Society


    There is a new society, that many of the ChEMBL-og readers may be interested in - The International Chemical Biology Society (ICBS). The first meeting is being held October 11-12th 2011 in Kansas City. The program looks great.

    Note: As of posting the ICBS website gives me, on my computer, a 'missing plugin' error, but other links seem to work.

  • USAN Watch - September 2011





    The September 2011 USANs have just been published.

    USAN Research Code


    Structure    		Drug Type Drug Class Target
    amitifadine, amitifadine hydrochlorideEB-1010, DOV-21947synthetic small moleculetherapeuticSERT, NET, DAT
    drisapersen, drisapersen sodiumGSK2402968A, h51AON23, PRO-051antisense oligonucleotidetherapeutic
    ganetespibSTA-9090synthetic small moleculetherapeuticHSP-90
    niraparibMK-4827synthetic small moleculetherapeuticPARP-1, PARP-2
    pasireotideSOM-230

    peptide    		therapeuticSSR
    prucalopride, prucalopride succinateR-093877synthetic small moleculetherapeutic5HT4
    samidorphan, samidorphan L-malateRDC-0313-00, ALKS-33natural product-derived small moleculetherapeuticOpioid receptors
    selexipagACT-293987, NS-304

    		synthetic small moleculetherapeuticprostacyclin receptor
    tanzisertibCC-930

    		synthetic small moleculetherapeutic
    JNK

  • Stem Cell Differentiation



    Over the summer one of our interns has entered some stem-cell differentiation into a small database - this is based on a literature search, followed by mapping the compounds to ChEMBL entries (or UniProt codes for protein factors). This was an Open Collaboration with Pfizer, who contributed the literature analysis, and also the mappings to the Cell Line Ontology. It is pretty fascinating to be able to control the path of differentiation with things that could potentially, one day, be drugs.

    So, we could put this up as a microsite, have the data available for download, etc, if there is any interest?