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Showing posts from September, 2013

Congratulations to Ben Stauch PhD!

Ben Stauch in the group has just been examined on his these - 'Methods for the Investigation of Protein-Ligand Complexes'. This was a tour de force of many techniques - NMR, computational and X-ray crystallography. Ben will be around for a few more months, writing things up, and completing/starting some experimental work on Xe complex refinement and characterisation.

Congratulations to Ben from all the group!

In due course, the thesis will be downloadable from the EBI and EMBL websites, and I'll update this post when the files are there.

jpo

Team ChEMBL in Action

We usually blog about exciting scientific and technological updates, interesting concepts, ideas and publications within the realm of life sciences and drug discovery. 
This post is slightly different, as it deals with something that might be (even) more important:  
A number of us in the ChEMBL Group (Rita (not in the picture above), Patricia, Felix, Anna, Sam, Anne, Mark, Michal, George, Gerard and Ashwini) are doing a Fun Run at Victoria Park on 12th October to help raise money for Cancer Research UK.  We are doing this to support a colleague who is currently receiving treatment for cancer.
We've set up a JustGiving page which makes donations fast, easy and secure.
Anything you can donate (in almost any currency :)) to this worthwhile cause would be really much appreciated.

The ChEMBL Group

Document Similarity in ChEMBL - 2

Following up on yesterdays post by George and Mark, I put together a slide, hopefully illustrating the advantages of document comparison using objects other than words alone.
jpo

Document Similarity in ChEMBL - 1

Many of you will have noticed a new section on the ChEMBL interface, specifically at the Document Report Card page, called Related Documents. It consists of a table listing the links for up to 5 other ChEMBL documents (i.e. publications aka papers) that are scored to be the most similar to the one featured in the report card. Here's an example
How does this work? There are examples of related documents sections online, e.g. in PubMed or in various journal publishers' websites. Document 'related-ness' or similarity can be assessed by comparing MeSH keywords or by clustering documents using TF-IDF weighted term vectors. Fortunately, ChEMBL puts a lot of effort in manually extracting and curating the compounds and biological targets from publications, so why not using these as descriptors to assess document similarity instead - as far as we know this is the first time this approach has been implemented?
So, here's how it works:
Firstly, for each document in ChEMBL, its…

Paper: Benchmarking of protein descriptor sets in proteochemometric modeling (part 2): modeling performance of 13 amino acid descriptor sets

A paper from Gerard in the group on some of his proteochemometric modelling work; a link to the paper is here. Z-scales rule! (the original Sandberg et alJ Med Chem paper on the Z-scales was one of my 'lightbulb turning on' moments in my professional life - go hunt it down if you don't know it.)

%T Benchmarking of protein descriptor sets in proteochemometric modeling (part 2: modeling performance of 13 amino acid descriptor sets %A G.J.P. van Westen %A R.F. Swier %A I. Cortes-Ciriano %A J.K. Wegner %A J.P Overington %A A.P. IJzerman %A H.W.T. van Vlijmen %A A. Bender %J J. Cheminformatics %D 2013 %V 5 %O doi:10.1186/1758-2946-5-42

jpo

New Drug Approvals 2013 - Pt. XIII - Dolutegravir (TivicayTM)

ATC code: J05AX12

On 12 August, the FDA approved a further drug for the treatment of HIV-1 infection, Dolutegravir (Tradename: Tivicay). Dolutegravir also known as S/GSK-1349575, is an HIV-1 integrase inhibitor. The drug has been approved for treatment of treatment-naïve as well as treatment-experienced HIV-infected adults including those who have been treated with other integrase inhibitors. In addition, Dolutegravir can be used for the treatment of children aged 12 years or older and weighing at least 40kg who have not been treated with integrase inhibitors, but are either treatment-naïve or treatment –experienced.
HIV, a lentivirus, infects vital cells in the human immune system such as helper T. cells (CD4+ T cells) and macrophages. The disease is responsible for millions of death every year, especially in Sub-Saharan Africa where treatment complications are enhanced by co-infection with tuberculosis and poverty. The approval of a new antiviral agent like Dolutegravir, will enhan…

Resources for Computational Drug Discovery - Wellcome Trust Course DEADLINE APPROACHING!

It's that time of year again when the ChEMBL team and their collaborators come together to host the "Resources for Computational Drug Discovery" course.
This course has been highly successful and well received over the past 3 years, and this year has no plans to be any different. It will be held here at the EBI campus in Hinxton, Cambridgeshire from the 9th - 13th December 2013.
We will have speakers and instructors from institutes such as the University of California San Francisco, Institute of Cancer Research and University of Sheffield. The course will have both theoretical and practical sessions where the attendees will have a chance to apply what they have just learned.
A provisional program can be found here.
The deadline to sign up is looming (8th October) so click here to register and avoid disappointment!

Louisa

New Drug Approvals 2013 - Pt. XIV - Tecfidera™

ATC Code: N07XX09(2014) Wikipedia:Dimethyl Fumerate ChEMBL: CHEMBL2107333
On March 27th the FDA approvedDimethyl Fumarate (DMF, trade name TECFIDERA™) for the treatment of adults with relapsing forms of multiple sclerosis (MS). DMF and the metabolite, monomethyl fumerate (MMF), activate the Nuclear factor (erythroid-derived 2)-like 2 (Nrf2) pathway via inhibition of Kelch-like ECH-associated protein 1 (KEAP1, cytosolic inhibitor of Nrf2). 
Target(s) The KEAP1 (CHEMBL2069156) is a naturally occuring cytosolic inhibitor of Nrf2 and DMF/MMF acts through chemical modification of KEAP1.

The NrF2 pathway is the primary cellular defence against the cytotoxic effects of oxidative stress. After translocation to the nucleus, Nrf2 heterodimerizes with MafF, MafG, and MafK. The combined heterodimer binds to antioxidant/electrophile response element (ARE/EpRE) and subsequently initiates transcription of these genes.

KEAP1 acts as the cytosolic anchor of Nrf2, sequestering Nrf2 in the cytoplasm during…

ChEMBL_17 Released

We are pleased to announce the release of ChEMBL_17. This version of the database, prepared on 29th August 2013 contains:

1,519,640 compound records1,324,941 compounds (of which 1,318,187 have mol files)12,077,491 activities734,201 assays9,356 targets51,277 documents
You can download the data from the ChEMBL FTP site. For more information please read the release notes.

Data changes since the last release:

Drug mechanism of action

For all FDA-approved drugs, information regarding the mechanism of action and associated efficacy targets has been curated from primary sources, such as literature and drug prescribing information. Targets have only been included for a drug if a) the drug is believed to interact directly with the target and b) there is evidence that this interaction contributes towards the efficacy of that drug in the indication(s) for which it is approved.

Metal-containing compounds

Structures for around 3200 metal-containing compounds have been removed from the database (thoug…