The ChEMBL-og

There is currently an opening for a Protein Computational Scientist to work on methods to assess and quantify the tractability (druggability) of potential new targets for drug discovery. This is a two year position funded by the Open Targets initiative. The appointee will work with scientists from the Open Targets partners to assess, validate and develop methods for quantifying target tractability with the ultimate goal of incorporating such methodologies into the target validation platform (https://www.targetvalidation.org/). The initial focus will be on “small molecule” tractability but we are also interested in other modalities in due course (e.g. antibody therapies). Many of the current methods to assess small molecule tractability are based on the use of 3D protein structures, but such information is only available for a subset of potential targets; a key component of the project is to determine robust methods and pipelines that can be applied to novel targets where there i...

We will be running a new series of webinars over the next few months. These will cover a range of topics including basic introductions to the Chemogenomics resources (ChEMBL, SureChEMBL, UniChem) as well as more detailed topics, a schema walkthrough and ChEMBL web services. The first webinar will be a basic introduction to ChEMBL and will be on 22nd February at 2pm GMT (3pm CET, 9am EST). If you would like to attend the webinar, please email to register . Please note, spaces are limited so please let us know as soon as possible if you register but are then unable to attend. We will post further details of upcoming webinars here, so watch this space! The ChEMBL Team

Wishing all of our many users and collaborators a very Merry Christmas and a Happy New Year! The ChEMBL Team

Within the ChEMBL database we spend a lot of time manually curating links between FDA approved drugs and their efficacy targets. With collaborators from the University of New Mexico and the Institute of Cancer Research, we have now published an analysis of these drug efficacy targets: Santos R, Ursu O, Gaulton A, Bento AP, Donadi RS, Bologa CG, Karlsson A, Al-Lazikani B, Hersey A, Oprea TI & Overington JP. A comprehensive map of molecular drug targets Nature Reviews Drug Discovery (2016) doi:10.1038/nrd.2016.230 In the article we address the complexities of assigning drug targets, describe the 667 human proteins and 189 pathogen proteins through which 1,578 FDA-approved drugs act and map each drug to its therapeutic indication via the WHO ATC classification system. We show that 70% of small molecule drugs still act through privileged families (GPCRs, ion channels, kinases and nuclear receptors), highlight the differences in innovation between different therapeutic areas,...

The latest ChEMBL database paper is now available online: http://nar.oxfordjournals.org/content/early/2016/11/28/nar.gkw1074.full This paper describes some of the additions to ChEMBL over the last few releases (ChEMBL_18 to ChEMBL_22) such as drug indications and clinical candidates, patent bioactivity data from BindingDB, drug metabolism information and richer assay annotation. A number of papers from our collaborators will also feature in the 2017 NAR database issue, so watch this space...

ChEMBL_22_1 data update: We would like to inform users that an update to ChEMBL_22 has been released.  The new version, ChEMBL_22_1, corrects an issue with the targets assigned to some BindingDB assays in ChEMBL (src_id = 37). If you are using the BindingDB data from ChEMBL, we recommend you download this update. This update also incorporates the mol file/canonical smiles correction announced previously. Updates have been made to BindingDB data in the ASSAYS, ACTIVITIES, CHEMBL_ID_LOOKUP, LIGAND_EFF and PREDICTED_BINDING_DOMAINS tables. Corrections have also been made to molfiles and canonical_smiles in the COMPOUND_STRUCTURES table. No changes have been made to other data sets or to other drug/compound/target tables in ChEMBL_22. The new release files can be downloaded from:  ftp://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/releases/chembl_22_1 A new version of the ChEMBL RDF is also available from: ftp://ftp.ebi.ac.uk/pub/databases/chembl/ChE...

The ChEMBL 22 release brings lots of new data. But we also released some new software so if you are interested in technical details please read on. 1. First of all, please note that ChEMBL 22 is the last release where we provide Oracle 9i dumps . Oracle 9i has been out of support now for at nearly a decade and shouldn't be in use anymore but please let us know if this is a problem. On the other hand, we will do our best to provide Oracle 12c dumps for the next release. 2. If you are using the python API client please upgrade it by running: [sudo] pip install -U chembl_webresource_client This will upgrade the client to the latest version which solves some minor bugs and adds an ability to search in document abstracts. It will also create a new cache so you will see new chembl data immediately. Otherwise, you will need to clear your cache manually. 3. New version ( 2.4.9 ) of the ChEMBL API has been released as well. This version includes:  - new endpoints: tissu...