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Showing posts from September, 2010

SGC's 1,000th Structure!

Congratulations to the SGC and their benevolent funders on the milestone release of their 1,000th structure 2XML . More details are available on the press release .

Opportunities to work with the ChEMBL team

We are anticipating engaging two/three contractors to work on a number of very exciting collaborative projects which will significantly augment the content and scope of the ChEMBL data. The work will be located at our facilities here at the Wellcome Trust Genome Campus (you will need to have existing right of residence and right to seek employment within the United Kingdom for these contractor positions), and we hope to start work before the winter holiday season. These offer the chance to work within a friendly, Open Access/Open Data team committed to developing novel and innovative precompetitive solutions for private and public sector drug discovery. We are looking for creative developers/scientists with existing skills covering significant elements of the following - perl/python, Linux, handling of biological and chemical structural data, ChEMBL, Matlab / Octave / R, MySQL / Oracle / SQL / PL/SQL, GO, MESH, blast, MVC development techniques, UniProt, Pfam, PDBe, Ensembl, Stitch,

ChEMBL Rocks!

Literally. It would be good to try and collect sites that have integrated, mirrored, processed, or derived online tools from the ChEMBL bioactivity data - we'll maintain a list of these on our website . Please mail us the url of any sites you know of, or if you would like listed?

GPCR SARfari Released

We are pleased to announce the release of GPCR SARfari . GPCR SARfari is a web based workbench focused on Class A G Protein-Coupled Receptors (Rhodopsin-like). The system currently contains: 912 protein sequences 546,467 bioactivity data points 118,834 compounds The bioactivty and compound data stored in GPCR SARfari has been taken from the latest release of the ChEMBL database. You can query this data directly via the interface, or download it from the links provided on this page . We have been collecting the protein structures of rhodopsin-like GPCRs and plan to add a structural component to GPCR SARfari. There will be a blog announcement providing more detail about this soon. The system is very similar to Kinase SARfari , so if you are familiar with the kinase version, you should have no problems navigating around GPCR SARfari. If there is enough interest we will also be happy to set up a webinar describing how to use both systems, please mail us in this is something

Papers: Ligand Efficiency Indices for Mapping Chemico-biological Space

A few months ago, Cele Abad-Zapatero visited our lab here at the EMBL-EBI, he touched all our lives in many ways and was a pleasure to have around. The sort of lab visitor anyone would welcome! Anyway, while here, we worked together on Cele's long-standing idea of an 'atlas' representation of target-chemical space, and a variety of descriptors will be incorporated into the ChEMBL database over the next few releases, both for visualisation, and also to enable data mining. %J Drug Discovery Today %T Efficiency Indices for an Effective Mapping of Chemico-biological Space: The Concept of an Atlas-like Representation %D 2010 %V 15 %P 804-811 %A Abad-Zapatero C. %A Perišić O. %A Wass J. %A Bento A.P. %A Overington J. %A Al-Lazikani B. %A Johnson M.E.

EBI Services User Survey

Would you consider completing the European Bioinformatics Institute (EBI) Survey at: It should take 10-15 minutes. There are no compulsory questions. You can be entered into a prize draw where you could win an iPad . This survey is collecting input from users and potential users of the EBI services.  We really value this input for development of our services, and want as many responses as possible.  We apologise if, in our enthusiasm, we have contacted you multiple times.  Please ignore the multiple contacts and forgive us! Otherwise, please visit  and complete the questions relevant to you. We will be collecting data until the end of September. Thank you for your help. (The picture is from the eponymous beta site).

Kinase SARfari Update

Kinase SARfari compound and bioactivity data has been updated using the latest release from the ChEMBL database. The compound count has increased from 28,223 to 33,559 and the bioactivity count increased from 146,865 to 212,735.

Lecture: Development and Applications of Computational Chemogenomics

We have a special visitor to the EMBL-EBI on Wednesday 10th of November - Didier Rognan of the University of Strasbourg at Illkirch. His presentation, on the "Development and Applications of Computational Chemogenomics" will be after lunch, so if anyone in the Cambridge area is interested in attending (campus staff will get a mail closer to the date, so please don't mail ;) ), please let me know (since I need to get you through security).

Books: Germ Stories

One of the great things about large meetings (I'm at the 50th meeting of ICAAC at the moment) are the publisher's stalls; the sort of specialist literature I like doesn't make conventional bookshops, and how bad is Amazon for recommendations for actually surprising and expanding your horizons and interests.... Anyway, we all have a little special someone in our lives, and this book, Germ Stories, is just for them. A set of delightful poems and rhymes about bugs, of all sorts, written by Arthur Kornberg  for his children. Education and entertainment for youngsters at it's best. High production values in the book - good quality binding, nice relief printed titling on the dust jacket, and delightful illustrations. A stylistic merging of Dr. Seuss with interesting subject matter, but in no sense is this nonsense. A must buy for all parents - especially at the show price of $20! %T Germ Stories %A A. Kornberg %D 2008 %I University Science Books %O ISBN-978-1-891389-5

ChEMBL PhD studentship Opportunites for Oct 2011 Intake

Registration in now open for applicants to the EMBL International Phd Programme ( EIPP ) for an October 2011 intake. We have potentially two positions available in the group, covering our general research interests , or an alternative project of your design. Students will be registered at the University of Cambridge , the highest rated university in the world (according to the QS World University Rankings 2010 ). Deadline for registration is December 1st 2010 . There are other colleagues at EMBL with an interest in Chemical Biology , and Bio- and Chemoinformatics, so please consider their research projects as well. Please, please, check the eligibility requirements carefully, and if you wish to mail with any specific queries or ideas please feel free to do so.

UK QSAR and Chemoinformatics Autumn Meeting Registration Now Open

It is impossible to underestimate the importance of drug discovery researcher community groups in the advance of drug discovery science in general, professional networking, and precompetitive and collaborative activities. A prime example is the UK QSAR and Chemoinformatics Group , who have been in existence since 1986. It is therefore a pleasure to host the Autumn 2010 meeting here at the EMBL-EBI , on Tuesday 12th October 2010 (there will be an informal meal, the evening before at a local hostelry for those interested). Finally, you don't have to work in the UK to attend! Registration (which is free) is now open at this link .

EMBL-EBI Small Molecule Bioactivity Course - Feb 2011

Just posted on the EMBL-EBI website are the first details of the Small Molecule Bioactivity Course . There will be more details later, and the agenda needs sketching out in more detail, but the dates, and guest lecturers are all set. So, if you would like to take part in an introductory level course to the use of chemogenomics approaches to understanding biology and supporting healthcare research, keep an eye out for more details, or take a chance in case all the places go, and register now! On a related note, I would like to highlight the overall good-all-round-goodness and helpfulness of Noel O'Boyle ; in honour, I may even go back to using the Irish form of my surname O'Verington..... The image above will mean little to most, but a lot to the few who watch UK kids TV.

ChEMBL_06 is live

We're pleased to announce the release, a few moments ago of ChEMBL_06. This contains an additional 29,142 compound records and 138,348 new bioactivities. We've also done quite a lot of compound cleanup, names, research codes ( vide infra ), and so forth. A variety of database dumps are available from the public ftp site, and the live web database is now connect to ChEMBL_06. Additional data this release includes the standard literature data, but also the data from the brilliant Genomics of Drug Sensitivity in Cancer project, coordinated by Ultan McDermott at the Sanger Center (interested readers in the oncology area are also pointed to this previous blog post ).

2010 New Drug Approval - Pt. XI - Alcaftadine (Lastacaft)

ATC code:  The summer got in the way of a timely post on this new drug. On 28 July 2010, Alcaftadine was approved for the treatment of patients with allergic conjunctivitis as a 0.25% opthalmic solution. This allergic reaction is most familiar in patients with hay fever but can also be caused by other allergens such as dust mites, moulds, perfumes etc . It causes red, itchy and watery eyes. Allergic conjunctivitis is caused by a type I hypersensitivity reaction of the immune system. Antigenic epitopes of the allergen are detected by IgE antibodies which mediate the excessive activation of mast cells and basophils .  The symptoms of allergic conjunctivitis are mainly caused by the release of histamine from these activated immune cells. Histamine increases the permeability of blood vessels and stimulates the activity of immune cells, through a number of differing histamine receptors. Alcaftadine and it's carboxylic acid metabolite (produced via a non P450 route) are anta