The ChEMBL-og

Dear future user, partner, collaborator or supporter! The ESFRI project EU-OPENSCREEN is an academic infrastructure initiative in Chemical Biology to serve your research needs. We are currently preparing the implementation of this pan-European infrastructure of open screening platforms to support basic and applied research. EU-OPENSCREEN will offer access to a unique compound library representing the know-how of European chemists, to a broad range of cutting-edge screening technologies, to valuable tool compounds for research, and to the knowledge that emerges from validated output of hundreds of screens stored and made publically available in a central database. We cordially invite you to join us in Oslo for an exciting science day where we inform about the progress of the project and the planned services with reports on the design of the joint European Compound Library, the screening services and the database. In particular, we would like to share with you your own experience...

Here's a free to enter competition for a brand new, fully working raspberry pi running the brand new chempi implementation . It includes everything you need to get started at home with ChEMBL - a sort of in silico Breaking Bad maybe (hopefully not, thinking about it). It includes everything you need, with the exception of a power supply and ethernet cable. We have run out of our creative juices, and cannot think of a suitable poem to mark the release of chempi - so the competition is for you to finish a limerick for us, starting with the line. There once was a hacker with chempi.... Entries must be posted in the comments section. Obscene or defamatory entries will be removed (all comments are moderated, so it may take a few hours for you entry to appear, so do not repost twenty times!). We haven't really decided how to pronounce chempi (with a hard 'k' start or a soft 'sh' start, just as with ChEMBL, both are used in the wild; and also does it rhyme...

One of the immediate consequences of refactoring our webservices using Django , Tastypie and related approaches (as described here ) is that we can run them on almost any database backend. Django abstracts communication with database and using custom QueryManagers we were able to implement chemisty-specific opererations, such as substructure and similarity search in a database agnostic manner. This means, that if we want, we can use only Open Source components (such as Postgres and RDKit ), or elect to use optimised commercially sourced software as appropriate. However, what if we go one step further and try to use Open Hardware as well? This is exactly what we've just done! We managed to install full ChEMBL 17 on raspbery pi . Some frequently asked questions (at lease those that have been asked internally) and technical details are below: 1. How much space does it take? 12 Gb, including OS, data and all relevant software. Unfortunately we a used 32 Gb SD card so this...

The USANs for October 2013 have recently been published. We have modified the sourcing of this data - using the new ChEMBL API to automatically parse the documents, extract and validate the mol files for the compounds. So in future, these reports should be more timely, complete and fun! USAN Research Code InChIKey (Parent) Drug Class Therapeutic class Target alectinib AF-802; CH-5424802 KDGFLJKFZUIJMX-UHFFFAOYSA-N synthetic small molecule therapeutic ALK apitolisib GDC-0980.1, G-038390, G-038390.1, RG-7422 YOVVNQKCSKSHKT-HNNXBMFYSA-N synthetic small molecule therapeutic MTOR,PI3K cimaglermin-alfa GGF2, rhGGF2 n/a protein ...

ATC Code:  C02KX   (incomplete) Wikipedia:   Macitentan ChEMBL:  CHEMBL2103873 On October 13th the  FDA approved   Macitentan  (trade name Opsumit  ® ) for the treatment of pulmonary arterial hypertension (PAH). Macitentan is an endothelin receptor antagonist (with affinities to both Endothelin ET-A (ETA) and Endothelin ET-B (ETB) receptor subtypes, similar in mechanism of action to the previously licensed drug Bosentan , CHEMBLID957 ). Target(s) The Endothelin receptor ET-A (ETA, CHEMBLID252  ; Uniprot P25101 ) and Endothelin receptor ET-B (ETB, CHEMBLID1785  ; Uniprot P24530 ) receptors mediate a number of physiological effects via the natural peptide agonist Endothelin-1 (ET1 , CHEMBL437472  ; Uniprot P05305 ). In addition to normal roles in supporting homeostasis, these effects can include pathologies such as inflammation, vasoconstriction, fibrosis and hypertrophy. Macitentan acts as an antagoni...

If you are a follower of this blog you will have seen some earlier posts ( here and here ) providing details on changes we are making to our Web Services. I recommend reviewing the previous posts, but in summary we have setup a temporary base URL to allow existing ChEMBL Web Service users to test the new ChEMBL API powered Web Services. The new temporary base URL is: https://www.ebi.ac.uk/chemblws2 As well as providing users with all existing functionality we have also added a couple of extra features, one of which is improved molecule rendering options. The current live Web Services provides the following REST call to allow you to get a molecule image:   https://www.ebi.ac.uk/chemblws/compounds/CHEMBL192/image     You are able to provide a dimension argument (pixels) to change the size of the image: https://www.ebi.ac.uk/chemblws/compounds/CHEMBL192/image?dimensions=200 The image quality has deteriorated, this is because the ima...

                                     We recently did some KNIME training for ChEMBL at a workshop, and it was very popular. It made us think a little about just how much was available within Knime for ChEMBL, and we thought we'd ask if there was interest in us running a specific, detailed course on ChEMBL/KNIME next year. So here's a poll. We'll keep this open for a month (i.e. closes 18th November 2013) and then decide what to do (if anything). The stoopid free poll server I sued doesn't like the browser safari - so I'll transfer across to another system over the weekend, and try and transfer votes. Thank you to those that have voted so far. Would you be interested in Knime ChEMBL training? Yes - I'd like a two day course at the EBI next year Yes - I'd like webinars Yes - I'd like you to visit our lab (charge involved) Yes - but not from you guys. No - Knime, what'...