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Showing posts from May, 2013

PhD positions available at EMBL-EBI

The joy in submitting a PhD is insurmountable, and some say it feels like going to heaven (n.b. Ben!).

Anyway, four EMBL-EBI faculty are recruiting PhD students in this round of the EMBL International PhD Programme. The deadline for submissions is 17th June 2013 - so not long away now - get your skates on if you are interested. These four year studentships will be available from October 2013 onwards.

The labs taking students this round are:

Alex Bateman's group.John Overington's group.Chris Steinbeck's group.Sarah Teichmann's group. Click on the links above to see current group research interests.

There are also other excellent PhD studentship opportunities available at EMBL in Heidelberg and various of the other EMBL Outstations - for details see here.

New Drug Approvals 2013 - Pt. VIII - Fluticasone furoate and Vilanterol (Breo ElliptaTM)

ATC Code:R03AK10

On May 10th, the FDA approved Vilanterol (Tradename: Breo Ellipta; Research Code: GW-642444M), a long-acting beta2-adrenergic agonist, in combination with the already approved fluticasone furoate, an inhaled corticosteroid, for the long-term maintenance treatment of bronchospasm associated with chronic obstructive pulmonary disease (COPD).
Chronic obstructive pulmonary disease (COPD) is characterised by the occurrence of chronic bronchitis or emphysema, a pair of commonly co-existing diseases of the lungs in which the airways become narrowed. Bronchial spasms, a sudden constriction of the muscles in the walls of the bronchioles, occur frequently in COPD.
Vilanterol is a new long-acting beta2 receptor agonist that through the activation of the beta2 adrenergic receptors present in the bronchial smooth muscle, leads to bronchodilation, and consequently eases the symptoms of COPD.
The beta2 adrenergeic receptor (Uniprot: P07550; ChEMBL: CHEMBL210) bel…

Paper: In silico applications of bioisosterism in contemporary medicinal chemistry practice

If you were looking for an up-to-date review of computational applications of bioisosterism in medicinal chemistry, then look no further. After an overview of the history and evolution of bioisosterism, the paper reports the various attempts aiming to capture and quantify it, as well as to disseminate its examples in the context of modern computer-aided drug discovery.
Link to the paper here
%A G. Papadatos %A N. Brown %T In silico applications of bioisosterism in contemporary medicinal chemistry practice %J WIREs Computational Molecular Science %D 2013 %O doi.10.1002/wcms.1148


New Drug Approvals 2013 - Pt. VII - Radium Ra 223 dichloride (Xofigo)

ATC code:

On May 15th, 2013 the FDA approved the alpha particle-emitting Radium Ra 223 dichloride (Xofigo) as a radiotherapeutic agent for the treatment of patients with castration-resistant prostate cancer, symptomatic bone metastases and no known visceral metastatic disease. The therapeutic component is the alpha particle-emiting Radium 223 isotope. It mimics calcium and binds to bone minerals is areas of rapid cell division, where it preferentially affects cancer cells. The radiation causes high levels of DNA double-strand breaks in adjacent cells, causing the killing of rapidly dividing cells, such as bone metastases.

After intravenous injection, Ra 223 is rapidly cleared from the blood and distributed primarily into bone or is excreted into intestine. The levels of radioactivity detected in the blood rapidly decrease and, at 24 hours, reach less than 1% of the administered dose. The alpha particle emission range of Ra 223 is 100 micrometers which protects against …

PKIS data in ChEMBL

The Protein Kinase Inhibitor Set (PKIS) made available by GSK was recently mentioned on In the Pipeline. In collaboration with GSK, we are making the data being generated on these compounds available via the ChEMBL database. We are also creating a portal for the compound set, where the structures can be browsed and downloaded, direct links to the data are provided and useful information can be posted. A preliminary version is available here: feedback would be appreciated.
The data generated on the PKIS set and deposited in ChEMBL may be downloaded in CSV format here (note that the Luciferase dataset described in the recent PLoS paper will be in the next release of ChEMBL). Alternatively, to view the data in the ChEMBL web interface, follow these steps: On the home page, enter 'GSK_PKIS' in the search box and click on the 'Assays' button...

On the 'Please select...' menu on the right, choose 'Display Bioactivities'...

Again, on the 'Please select...'…

ChEMBL_16 Released

We are pleased to announce the release of ChEMBL_16. This version of the database was prepared on 7th May 2013 and contains:

1,481,473 compound records
1,295,510 compounds (of which 1,292,344 have mol files)
11,420,351 activities
712,836 assays
9,844 targets
50,095 documents
19 activity data sources

You can download the data from the ChEMBL ftpsite and do not forget to read theChEMBL_16 Release Notes

Data changes since the last release
ChEMBL_16 includes the Millipore Kinase Screening publication (CHEMBL2218924), which is kinase screening panel data set focused on 158 known kinase inhibitors and the OSDD Malaria Screening dataset (CHEMBL2113921), which is a set of anti-malarial compounds and bioactivity data provided by the OSDD Malaria consortium
In addition to the our regular publication and dataset updates we are now also loading supplementary bioactivity datasets. In this example the original paper from GSK was published in 2010 (CHEMBL1157114) and with the release of ChEMBL_1…


We would like to draw attention to readers of The ChEMBL-og to an excellent new paper in the Journal of Cheminformatics, describing the work of Egon Willighagen and co-authors in building the first published, publicly available version of ChEMBL data in RDF form (ChEMBL RDF). The paper also provides details on a number of linked data based applications built on top of an RDF data model, demonstrating the benefits of the data transformation. More details about the paper are provided here and the link to the paper is here.

%T The ChEMBL database as linked open data %A E.L. Willighagen %A A. Waagmeester %A O. Spjuth %A P. Ansell %A A.J. Williams %A V. Tkachenko %A J. Hastings %A B. Chen %A D. J Wild %J J. Cheminf. %D 2013 %V 5 %O doi:10.1186/1758-2946-5-23
The ChEMBL group have been funded by the IMI OpenPhacts project to build and deploy an RDF version of ChEMBL (which we are currently calling ChEMBL ChEMBL RDF, sorry for the confusion!). With changes in content and curation closely co…

New Drug Approvals 2013 - Pt. VI - Gadoterate Meglumine (DotaremTM)

ATC Code: V08CA02
Wikipedia: Gadoteric Acid

On March 20th 2013, FDA approved Gadoteric Acid (as the meglumine salt; tradename: Dotarem; research code: P 449; CHEMBL: CHEMBL2219415), a gadolinium-based contrast agent (GBCA) indicated for intravenous use with magnetic resonance imaging (MRI) in brain (intracranial), spine and associated tissues of patients ages 2 years and older, to detect and visualize areas with disruption of the blood brain barrier (BBB) and/or abnormal vascularity of the central nervous system (CNS).

When placed in a magnetic field, Gadoteric Acid develops a magnetic moment. This magnetic moment enhances the relaxation rates of water protons in its vicinity, leading to an increase in signal intensity (brightness) of tissues. Gadoteric Acid enhances the contrast in MRI images, by shortening the spin-lattice (T1) and the spin-spin (T2) relaxation times.

Other GBCAs have already been approved by FDA for use in patients undergoing CNS MRI and these include Gadopentetate D…

Compiling inchi-1 to JavaScript

There are more and more software libraries being ported to JavaScript. The best example is JavaScript/HTML5 Citadel demo of the Unreal Engine. So why not to try with some chemical stuff? One of the most important chemical software libraries is IUPAC InChi. It's also extremely hard to reimplement as it's written in low-level, functional-style C. On the other hand it's just a few headers and source files, without any dependencies so it's a perfect use case for Emscripten.
Emscripten 'is an LLVM-to-JavaScript compiler'. It can be used as a drop-in replacement for standard tools such as gcc or make. Recently it got support for asm.js - optimizable, low-level subset of JavaScript.
I wasn't the first to come up with this idea - one of our local heroes, Noel O'Boyle wrote a set of articles about translating the InChI code into JavaScript on his blog. I didn't know about his work during my experiments, which is good, because I took slightly different approach…

Direct submissions of data to ChEMBL and the Open PHACTS project

The world of the ChEMBL-og

The map above shows the google analytics map view of the users of the ChEMBL-og. Being the completist that I am, it always bugs me, that there are still quite a few places that don't know about the ChEMBL-og. So if you have some friends in those lonely grey countries, such as Greenland, North Korea, Mali, Niger, Chad, Gabon, Central African Republic, DR Congo, etc. Tell them about the ChEMBL-og!


PhD Studentship at Babraham - Systems Pharmacology Models of Druggable Targets and Disease Mechanisms

Our friendly neighbours at The Babraham Institute are looking for a PhD candidate to work on systems pharmacology models, as part of a collaboration between the Le Novère (Babraham), the Hermjakob (EMBL-EBI) and the pharmaceutical company GlaxoSmithKline. The Le Novère groupuses quantitative computational models to understand cellular and molecular processes, and develop community services that facilitate research in computational systems biology (

One of the major challenges of drug discovery is to demonstrate the efficacy of a potential new drug. This goes beyond the development of a potent molecule - it also implies a good understanding of the biological context, how it relates to a particular disease, and the drug's mechanism of action. The availability of relevant Systems Pharmacology models can therefore have a significant impact. The most comprehensive repository of Systems Biology models in machine readable language is BioModels Database, created by …