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Showing posts from October, 2010

Contractor Positions Within ChEMBL

As mentioned in a previous post, we now have some immediately available positions within our team for some short-term contractors (6 months to 1 year). These are for two collaborative (and very exciting) industry projects, and require good bioinformatics knowledge, programming in perl (or equivalent) knowledge of SQL, and database querying and integration. Previous experience in either target assessment, or computational studies of ADMET processes would be greatly beneficial (see below).

One position will be to work on 'druggability' calculations, the second will be connected with comparative genomics of ADMET systems - building a prototype ADMET SARfari (see the SARfari tags on the ChEMBL-og for more details on SARfari). Positions are full time and require a pre-existing right of residence and also pre-existing right to work within the United Kingdom. Pay and general conditions are subject to negotiation. Work will be based at our Hinxton campus site. More details are availab…

Staff Post in ChEMBL - EU-OPENSCREEN Database developer

We will soon post on the EMBL recruitment pages, details of a new post within ChEMBL - a database developer for a very exciting pan-European collaboration called EU-OPENSCREEN. EU-OPENSCREEN is one of a set of large-scale Research Infrastructure projects called 'ESFRIs', and EU-OPENSCREEN is connected with establishing an infrastructure of screening centers, compound collections and associated 'Open' Chemical Biology Data. EU-OPENSCREEN has recently started, and is in the so-called 'Preparatory Phase'.
The job will require someone with good technical informatics and scientific skills connected with database design and integration, biological screening, bioinformatics and chemoinformatics, data security, and will require travel to European and U.S. collaborator labs. 
An associated EU-OPENSCREEN post within the Steinbeck group at the EBI, on Data Standards, Ontologies, etc., will also be announced shortly.
When the position is live on the EMBL recruitment site, I&#…

Internships within ChEMBL

We regularly offer internships within the ChEMBL group, these are typically for between three and six months. We receive about five to ten applications per week, so only a small fraction of applications are successful. We try and match these against project ideas we have, available space, and our limited budget. Here is some advice for those wishing to apply.

Please note - working as an intern at any EMBL lab may negatively affect applications for study as a PhD student at EMBL - please check the regulations carefully if you plan to apply for a PhD.
Please try and be accurate about the group you are applying to, we understand that you are probably looking at many opportunities, but if you mention a completely different scientific area, PI name, or have a very vague and general application, we will be unable to consider your application further.Attach a current and accurate cv (please do not feel under pressure to limit this to two pages) with your initial application. Be accurate with t…

ChemSpider links now available in ChEMBLdb

Here at ChEMBL, we are often contacted by users who are interested in purchasing some of the compounds that we store in our databases. However, our compounds are curated directly from the literature and we do not have access to physical samples. To enable our users to find supplier information for the compounds, we have now added direct links from ChEMBL to ChemSpider. ChemSpider is a resource containing millions of chemical structures, with associated property information. This property information also includes supplier information, where available. You can connect to ChemSpidervia our Compound Report Card, under "Database Links" and by clicking on the Standard InchiKey hyperlink you will be taken directly to the same compound in ChemSpider. You can also connect directly to ChEMBLdb via ChemSpider using the hyperlink found under their "Biological Data" tab.

ChEMBL_07 Downloads Available

Following last weeks announcement regarding the release of ChEMBL_07, we are now pleased to say the downloads are available on the ftpsite.

2010 New Drug Approvals - Pt. XII - Pegloticase (Krystexxa)

ATCC: M04AX02

On September 14th 2010, the FDA approved Pegloticase under the trade name Krystexxa. Pegloticase is a recombinant enzyme for the treatment of gout and can replace xanthine oxidase (XO) inhibitors for patients who do not respond to or cannot tolerate treatment with xanthine oxidase inhibitors. 

Gout is a painful affliction caused by microscopic needle-shaped crystals of sodium urate which precipitate in joints and tendons and stimulate a local inflammatory response. These attacks of inflammatory arthritis not only cause pain and stiffness of the joint, but, if left untreated for years, also damage the cartilage and surrounding tissue. Hard, non-painful deposits of crystalline uric acid known as tophi occur in the joints and sometimes the kidney. 

Gout is generally associated with obesity, hypertension, insulin resistance and hyperlipidaemia. In more than half of the cases of diagnosed gout, patients have elevated blood levels of uric acid.

Conventionally, acute gout at…

DrugEBIlity - Structure-based component

Following some successful initial testing and feedback, we have opened up the Structure-based scoring component for full Open Access - please be aware that this is still be considered to be in a test phase, since the coding pixies are still tinkering away in the background. This used to be known as Strudle, which is a name we will not use externally for structure-based assessment methods - The overall name for the druggability services from the ChEMBL group at the EMBL-EBI will be known as DrugEBIlity - cool name eh? It's got EBI in there, obeys a reasonable linguistic construction (it may even be a heterograph, but I'm not sure), is an atrocious pun, and states our view that drugability has one G. Remember that there is a capital I next the the lowercase l.....

The current portal allows you to search with a sequence, with a PDB code, or to upload a structure of your own. We are still establishing a reasonable capacity and farm priorities for uploaded structures, so please be …

ChEMBL licensing

The data content in ChEMBL is licensed under a highly permissive Creative Commons license - specifically the "CC Attribution-ShareAlike 3.0 Unported license"

The required attribution should contain the url of the ChEMBL resource, and also the release version, e.g.:

ChEMBL data is from http://www.ebi.ac.uk/chembl - the version of ChEMBL is ChEMBL_07.
This should be visible on the entry portal for a web resource in which ChEMBL is integrated, or contained with the documentation for any further distribution.

2010 New Drug Approvals - Pt. XIII - Fingolimod (Gilenya)

ATC code: L04AA27
On September 21st, the FDA approved Fingolimod (previously known as FTY-720) for the treatment of relapsing forms of multiple sclerosis (MS). Fingolimod is marketed under the name Gilenya and is the first oral drug that can slow the progression of MS.

MS is a chronic autoimmune disorder affecting the central nervous system (CNS) and causing a broad spectrum of neurological symptoms ranging from numbness of the limbs and muscle weakness to cognitive impairment, depression, and a broad spectrum of other disorders. People suffering from MS experience inflammatory reactions which damage the myelin sheath surrounding the axons of nerve cells. The inflicted lesions impair the transmission of action potentials and ultimately perturb normal function of the CNS.

Upon administration, Fingolimod is phosphorylated by sphingosine kinase (Uniprot: Q9NRA0) to form the the active metabolite Fingolimod-phosphate - Fingolimod is therefore a prodrug. Fingolimod-phosphate binds the sph…

ChEMBL_07 is now live

Continuing the pattern of short blog posts (lots of overdue paper reviews and grants to do), ChEMBL_07, containing 2,948,069 bioactivities has just been attached to the web front end. Database dumps for the ftp site are being prepared now, and will be available, once tested, next week.

ChUG - The Chembl User Group

So,we are just starting to plan the first ChUG meeting - if you are interested, get over to the ChEMBL User Group LinkedIn group.