The ChEMBL-og

ADME studies are focused on understanding the disposition of a compound within an organism and the results of such studies play a critical role in the drug development process. ADME studies (more commonly referred to as pharmacokinetic or PK studies) are focused on 4 main areas: Absorption, Distribution, Metabolism and Excretion. More information on the PK measurement types can be found here . Comparisons of PK data across species is a potential problem drug researchers need to deal with, as model organism studies are the primary source of such data. For example, in an animal model study, which may be carried out on a compound as it passes through the drug development pipeline, is it meaningful to compare clearance or bioavailability data from a mouse or rat to human? Clearly there are many differences (physical, metabolic, genetic,..), which make answering these types of questions difficult. Building tools which guide researchers to potential answers or pr...

We would like to announce the release of new version Kinase SARfari. The latest version has been updated using the chembl_12 data, which contains: Bioactivity datapoints: 503041 (+15%) Compounds: 54189 (+6%)   Various dumps of the data from Kinase and GPCR SARfari are also downloadable from the download page.  Of course, we welcome feedback from our users!

Not Moon Safari but Kinase SARfari ! There are a lot of changes to the interface and integration of data, and also oodles more data (104% more) contained in the latest release. These include: Unified SARREGNOs to CHEMBL IDs (also Assay & Doc ids). Updated assays, activities and compounds from ChEMBL_10. Added 30 non-human kinase domains. Calculated site similarity distances and neighbourhood density (ND) scores between all kinase domains. Added Drug Icons into the interface. Added links to ChEMBL Target/Doc/Assay Report Cards. Renamed old sources (drugstore & candistore). Contents: Kinase domains: 989, Kinase bioactivity datapoints: 435,873, Kinase compounds: 51,090. For the time being, the new version can be found on our dev site at http://wwwdev.ebi.ac.uk/chembl/sarfari/kinasesarfari . As always, we would appreciate any bug reports, feedback, etc .

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 ...

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.

New data and a slightly remodelled interface for Kinase SARfari are now available here. Key changes are: Loaded chembl_02 data - Compound count increased from 17,028 to 28,223 and Bioactivity count increased from 68,861 to 146,865 Compound selected sets updated - 10 Drugs compounds, previously 7, and 258 Clinical Candidates, previously 53 Interface updated with EMBL-EBI standard styling Added Download section to interface

A new data load for kinase SARfari screening data has just been completed. There is a significant growth in both the number of inhibitors (28,016 vs. 17,028), and the number of assay data-points (147,478 vs. 68,861). It is available here Remember it is a test version only, and if you do find any problems, please mail them... Finally, there is a funny story behind the picture, which will emerge over the next few blog posts.

The following is written in Japanese.... ケンブルチーム(ChEMBL Team)は、欧州バイオインフォマティクス研究所( EMBL-EBI )にあり、創薬研究に有用な化合物やターゲット情報を提供するデータベースを開発しています。 ChEMBLdb は、創薬研究に有用な医薬品化合物の情報を提供するデータベースです。現在、約50万個の化合物情報、約190万件の活性情報及びそれらのターゲット情報が登録されています。ユーザーは、生物活性化合物の情報を部分構造検索や類似性検索で調査したり、また、ターゲットのアミノ酸配列からBLAST検索でアッセイ情報を収集することができます。 ケンブルチームでは、キナーゼに特化したカイネースサファリ( Kinase SARfari )のサービスも開始しました。 日本語でのご質問、ご要望は kaz(at)ebi.ac.uk までどうぞ。チームメンバー一同、皆さんのご利用をお待ちしています！

The Kinase SARfari interface has been updated and is now using the JME Molecular Editor for compound drawing and editing. JME is an easy to use fast loading applet, for more information visit: http://www.molinspiration.com/jme/

Kinase SARfari is now live and online - free and open to one and all. We'll keep an eye on machine logs for the next couple of weeks, and so we may bounce it now and then. Please let us know if you have any issues with using it, and please tell us OS and browser versions for any bug reports. The URL for kinase SARfari is http://www.sarfari.org/kinasesarfari Full source code is also available, licensed under a very permissive Creative Commons licence. Mail us if you want this, but as soon as we sort out our downloads area, it will also be available from there. The data in the backend database is in the process of being updated to a more recent data cut, and when this is done, we'll post details. We're also resurrecting the rhodopsin-like GPCR version. There is also an email address for sarfari support issues .

We are testing a number of interfaces to our data at the moment, and have just flipped Kinase SARfari to a public facing server. We are looking for some people willing to test the interface on a number of differing platforms, so if you are interested, please mail us . An install package is also available, for those wishing to try things on their own machines (however, you'll need some experience in web server config, Catalyst (the MVC, not the modelling package), an Oracle database, and a chemical data cartridge...)

We have had quite a lot of recent interest in our Kinase SARfari chemogenomics system . Click the previous link to get an overview. So for those interested, there will be a web meeting at Friday July 31st at 2pm (UK local time, which at this time of year is BST). Mail us for the web link and phone conference details.