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Showing posts from August, 2012

ACS Philadelphia (posted by Louisa)

I (Louisa) will be attending the ACS national meeting in Philadelphia, which opens this Sunday afternoon (19th August). If anyone would like to meet with me to discuss ChEMBL or learn more about what we do, please feel free to email me at . Providing that my hotel has internet, I shall be able to respond and organise something. Additionally, if you see me wandering around the conference, probably picking up free pens, please stop me for a chat. It's always nice to meet our ChEMBL users.

Paper: Annotating Human P-Glycoprotein Bioassay Data

A paper on extraction, curation and comparison of literature data for a key transporter in drug discovery P-glycoprotein Uniprot:P08183 (aka MDR1, pgp, etc ). It details some interesting comparisons of different assay formats, readouts, cell-backgrounds and so forth. Here's a link to the paper (It should be Open Access, but isn't at the moment :( ). %T Annotating Human P-Glycoprotein Bioassay Data %J Mol. Informatics %A B. Zdrazil %A M. Pinto %A P. Vasanthanathan %A A.J. Williams %A L.Z. Balderud %A O. Engkvist %A C. Chichester %A A. Hersey %A J.P. Overington %A G.F. Ecker %D 2012 %V 31 %O DOI: 10.1002/minf.201200059

Webinar: Accessing ChEMBL Web Services via Workflow Tools.

This is gentle reminder for the forthcoming webinar on accessing  ChEMBL REST web services via KNIME and Pipeline Pilot  at  3.30 pm BST  on Wednesday,  8th August 2012  (aka  tomorrow ) . Please  email  me in advance in order to register for this.


With the aim of providing more options to access the ChEMBL database, a PostgreSQL version of the most recent ChEMBL release is now available on the ChEMBL FTP site , (thanks to the Ora2Pg project for making the conversion process relatively painless).  The main goal of this project is make it easier for users to integrate the chemical data in the ChEMBL database with freely available chemical cartridges, such as the excellent RDKit and Bingo . Now that we have the PostgreSQL version of the database available, we are in the process of benchmarking the aforementioned chemical cartridges - we will report back soon the results of the benchmarking exercises we are undertaking. We are also looking to build and release a virtual machine, which will come preloaded with ChEMBL, PostgreSQL, RDKit and/or Bingo. When we have more details on this we will let you know. Right now everyone has the opportunity to download and install the PostgreSQL version of the ChEMBL database

Books: Assay Guidance Manual

Came across this great online book, developed jointly by researchers from Eli Lilly, and staff from the NIH - it's a great overview of the factors and methodology of HTS and SAR measurements, and provides a great orientation for new researchers interested in the field. Here's the text from the book web page .... The collection of chapters in this eBook is written to provide guidance to investigators who are interested in developing assays useful for the evaluation of collections of molecules to identify probes that modulate the activity of biological targets, pathways, and cellular phenotypes. These probes may be candidates for further optimization and investigation in drug discovery and development. Originally written as a guide for therapeutic project teams within a major pharmaceutical company, this manual has been adapted to provide guidelines for scientists in academic, non-profit, government and industrial research laboratories to develop potential assay f