ChEMBL Resources

Resources:
ChEMBL
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SureChEMBL
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ChEMBL-NTD
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ChEMBL-Malaria
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The SARfaris: GPCR, Kinase, ADME
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UniChem
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DrugEBIlity
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ECBD

Thursday, 16 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 chembl-help@ebi.ac.uk. 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.

Thursday, 9 August 2012

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

Tuesday, 7 August 2012

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.

Monday, 6 August 2012

ChEMBL PostgreSQL



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 and optionally install a chemical cartridge. We hope this will help as many projects as possible and any comments or feedback will be very much appreciated. Enjoy it :)

(You can download the ChEMBL_14 PostgreSQL here, the tarball also comes with some basic install instructions, but does assume you have a PostgreSQL instance up and running).

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 formats compatible with High Throughput Screening (HTS) and Structure Activity Relationship (SAR) measurements of new and known molecular entities. Topics addressed in this manual include:
  • Development of optimal assay reagents.
  • Optimization of assay protocols with respect to sensitivity, dynamic range, signal intensity and stability.
  • Adopting screening assays from bench scale assays to automation and scale up in microtiter plate formats.
  • Statistical concepts and tools for validation of assay performance parameters.
  • Secondary follow up assay development for chemical probe validation and SAR refinement.
  • Data standards to be followed in reporting screening and SAR assay results.
  • Glossaries and definitions.
This manual will be continuously updated with contributions from experienced scientists from multiple disciplines working in drug discovery & development worldwide. An open submission and review process will be implemented in the near future on this eBook website, hosted by the National Library of Medicine with content management by the National Center for Advancing Translational Sciences (NCATS, http://ncats.nih.gov/), the newest component of the National Institutes of Health (NIH).

%T Assay Guidance Manual
%D 2012
%E G.S. Sittampalam
%E N. Gal-Edd
%E J. Weidner
%E D. Auld
%E M. Glicksman
%E M. Arkin
%E A. Napper
%E J. Inglese
%I Eli Lilly & Company and the National Center for Advancing Translational Sciences
%O http://www.ncbi.nlm.nih.gov/books/NBK53196/
%O Bookshelf ID: NBK53196
%O PMID: 22553861