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Showing posts from March, 2013

Meeting up at the ACS in New Orleans

A couple of us are out in New Orleans for the ACS in a few weeks - if any ChEMBL users would like to meet up to get some training, ask questions, suggest improvements to what we do, or just grab a beer or coffee, we'd be very happy to do so. We arrive Sunday and leave Tuesday night.

The picture is rather amusing, and looks a little like Mark and me, sort of. Credit for image is detailed in the image itself.....

jpo and mark

Paper: Brain: Biomedical Knowledge Manipulation

There's a paper just out from Samuel, one of the PhD students in the group - the link to the Open Access paper is here. Brain is a Java software library facilitating the manipulation and creation of ontologies and knowledge bases represented with the Web Ontology Language (OWL).

%A S. Croset %A J.P. Overington %A D. Rebholz-Schuhman %D 2013 %T Brain: Biomedical Knowledge Manipulation %J Bioinformatics %V 29 %O DOI:10.1093/bioinformatics/btt109 %O PMID:23505292

New Drug Approvals 2013 - Pt. IV - Ospemifene (OSPHENA®)

ATC Code: Not Assigned Wikipedia:Ospemifene
On February 26, FDA approved Ospemifene (Trade Name: OSPHENAPubChemCID 3036505ChEMBLCHEMBL2105395, ChemSpider2300501) for the treatment of moderate to severe Dyspareunia - symptom of vulvular and vaginal atrophy due to menopause.
Dyspareunia, is pain during or after sexual intercourse. It can affect men, but is significantly more common in women, affecting up to one-fifth of women at some point in their lives. Women with dyspareunia may have pain in the vagina, clitoris or labia. This may be due to medical or psychological causes. There are numerous medical causes of Dyspareunia, like : Vaginismus, Pelvic Inflammatory Disease, Genital or Pelvic Tumors, Urethritis, Urinary Tract Infection, Vaginal Atrophy, Vaginal Dryness, Vulvar Cancer, Childbirth Trauma (postpartum), Skin Conditions (Lichen Sclerosus, Lichen Planus, Eczema, Psoriasis), Female Genital Mutilation, Endometriosis  - many of which can be treatable.


Ospemifene is a novel se…

The results are in - inorganics are out!

A few weeks ago we ran a small poll on how we should deal with inorganic molecules - not just simple sodium salts, but things like organoplatinums, and other compounds with dative bonds, unusual electronic states, etc. The results from you were clear, there was little interest in having a lot of our curation time spent on these. We will continue to collect structures from the source journals, and they will be in the full database, but we won't try and curate the structures, or display them in the interface. They will be appropriately flagged, and nothing will get lost. So there it is, democracy in action.

So for ChEMBL 16 expect fewer issues when you try and load our structures in your own pipelines and systems.

Thanks for all your input.

jpo

Registration for diXa course "Microarray Analysis using R and Bioconductor" is now open

USAN stem searching within ChEMBL

Here's a little tip that may be of some use to you. The compound name search feature will also match substrings, so it is easy to type in a USAN/INN stem, and then retrieve all matching compounds - for example, "gliptin" will retrieve all DPP-IV inhibitors with non-proprietary (formal) names. This is pretty useful - of course the substring search functionality is not restricted to USANs/INNs.

A list of the current USAN stems is here. Note, they were never designed to be orthogonal, so the low complexity ones will give a lot of false positives.....

Group Leader/Postdoc positions in selective kinase inhibitor design

One of our Industry Programme members passed on a listing for some positions they are looking to fill at the new center in Heidelberg - BioMed X. It looks like it may be of interest to many of the ChEMBL-og readers, so I thought I would post it here....

They are looking for a Computational Chemistry/Drug Design group leader for a project "Development of a design software of SELECTIVE kinase inhibitors". The BioMed X Innovation Center in Heidelberg, Germany, constitutes a new class of incubator at the interface between academia and industry where top life science talents from all over the world are jointly working on biomedical innovation outside the pharma box. Young talents from leading academic institutions world-wide are selected in annual assessment centers based on their scientific expertise, creative energy, and passion for product-oriented pre-clinical research & development. Interdisciplinary project teams are collaborating in an open-innovation lab facility in He…

To Remove Or Not To Remove - That Is The Question

During the course of standard compound curation, I come across problem inorganic compounds. An example of these are Cisplatin and Transplatin. These compounds only differ in the orientation of their complex bonds but complex bonds cannot be drawn in a standard molfile without causing InChI issues. At the  moment, they are kept separate by showing standard bonds between the Pt, Cl and NH3 in Cisplatin, but we have removed the bonds altogether for Transplatin. This is not an ideal situation, nor an accurate structural representation.

Another example is the compound, below left, and how it should look as a complex, right, from the paper:



At the moment, there are approximately 1,800 cases like this, which only accounts for 0.15% of the entire ChEMBL compound set.

What we are proposing to do is to remove the structures for these complex compounds and to keep only their names and all of the associated biological data. This would then treat them in a similar way to the antibodies and large …

New Malaria-Data release

We are very pleased to announce that a new release of the malaria-data resource (MMV_2) is now freely available here
The release was prepared on 1st March 2013 and contains: 362,845 compound records280,985 compounds3,288,801 activities190,243 assays5,431 targets24,200 documentsThe database contains several new datasets, including OSDD, Harvard and WHO-TDR Malaria screening data. Furthermore, the new interface has adopted the new look and feel features recently introduced  in the main ChEMBL interface, such as the redesigned search hits tables and document report card.
As usual, the interface provides compound, assay and target keyword search capabilities, as well as structure-based and sequence-based search functionality for compounds and protein targets respectively. Finally, structure look-ups are offered out-of-the-box via the UniChem cross-references. 
Please see MMV_2_release_notes.txt for full details of all changes in this release.
This is probably the most comprehensive public ma…