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Showing posts from July, 2010

Webinar - Installation and setup of a MySQL instance of ChEMBL

We are planning to run a web tutorial on the installation and set-up of a local MySQL version of ChEMBL. This will allow very flexible querying of the data within ChEMBL (with the exception of chemical structure searching for which there is currently no freely available cartridge/plugin (yet)). We will do an entire download and install of MySQL, download of the ChEMBL data, and setting everything up, then doing some sample queries - all within one hour.

The web meeting will be from 3pm to 4pm UK time (we are on BST at the moment) on Thursday 5th August. Please mail us if you want a link to the web-meeting, and the toll-free dial-in number. Please, (please), do not edit the title on the mail message link.

From One Of Our Collaborators - CanSAR

One of our collaborators, Bissan Al-Lazikani is building a highly integrated system for cancer target and drug discovery - canSAR. A pre-release of the Target and Drug Synopsis pages is now available, populated with the Genomics of Drug Sensitivity Project at the Wellcome Trust Sanger Institute, canSAR complements the annotation of the 1000 cell-line screening project.

Due to the pre-release nature of this component of canSAR, many features have been disabled and removed. The full public release of canSAR will be available later in the year (it is very cool though!).

canSAR is developed and hosted by the Cancer Research UK Centre for Cancer Therapeutics at the Institute of Cancer Research.

Interest in a ChEMBL User Group (ChUG) meeting?

We are now amassing a reasonably sized group of users for the ChEMBL database, both for the web interface, SARfari and local install versions. We are discussing holding a user group meeting on campus here at Hinxton, for early 2011, probably in January or February.

Please see the poll below....


We would also be interested to hear from one or two of our user-base to help plan and coordinate the event - if this sounds like you, please mail me.

P.S. We are also planning to hold another week long training course for ChEMBL resources next year, so keep an eye on the blog if you are interested in this.

Please note - the poll is now closed. We will try and arrange something in January or February next year, and would the people who were interested in helping us organise the meeting please make themselves known!

EMBO Chemical Biology Meeting 2010

The 2010 EMBO Chemical Biology meeting to be held in Heidelberg is shaping up very well - excellent speakers, really exciting portfolio of international chemical biology research, etc, but it is now only two months away, however some places are still available for attendees. Links to the conference details are here.

Of course, several of the ChEMBL group will be there, and so if you'd like to meet any of us there, hear about our plans for the databases, or know more about research, drop us a line.

EMBL Postdoctoral Programme - Interdisciplinary Postdocs (EIPOD)

EMBL run an annual round of inderdisciplinary postdoc applications, with the research either from a set of pre-defined projects, or for projects of the applicants design. The positions reply on extensive collaboration between EMBL faculty, to produce an innovative and cutting-edge research opportunity. The deadline for applications to the EMBL EIPOD program is 5pm 31st August 2010. Details are at the following link, and we would welcome any applicants wishing to discuss potential projects with us.

Chembl_05 released

We are pleased to announce the immediate release of chembl_05, accessible through the front-end (at www.ebi.ac.uk/chembldb) and also available on the anonymous ftp server (ftp://ftp.ebi.ac.uk/pub/databases/chembl/). This release contains 7,493 targets, 697,730 compound records, 578,715 distinct compounds, 2,787,240 bioactivities abstracted from 36,624 publications. This correpsonds to a growth of 3% in bioassay count compared to chembl_04.

2010 New Drug Approvals - part IX - Sipuleucel-T (Provenge)

On April 29th, the FDA approved Sipuleucel-T (Tradename: Provenge, REsearch Code: APC-8015) a highly novel treatment (a cell-based vaccine) for hormone refractory (castration resistant) prostate cancer. Patients with this form of late-stage prostate cancer have refractory metastases after hormonal therapy even though they may have few symptoms. Sipuleucel-T has had a complex development and approval history (as a google search will readily show). Sipuleucel-T is a mixture of white blood cells that are extracted from the patient through a process called Leukapheresis, which is routinely used to isolate white blood cells e.g. for diagnostic purposes. In the 3 days that pass between the extraction of the white blood cells from the patient and the treatment with sipuleucel-T, the mixture is activated by exposing the extracted cells to an engineered protein called PAP-GM-CSF. In this, PAP stands for prostatic acid phosphatase (Uniprot P15309), which is produced in high amounts by metast…

2010 New Drug Approvals - part VIII - Cabazitaxel (Jevtana)

ATC code (partial): L01CD
The FDA approved Cabazitaxel on June 17th. Cabitaxel is used in combination with prednisone to treat advanced, hormone-refractory prostate cancer.

Typically, prostate cancer occurs in older males and is among the most common forms of cancer affecting men with around 200,000 new cases per year diagnosed in the United States. Prostate cancer is a glandular cancer that is generally slow-growing. However, prostate cancer develops the ability to penetrate into other tissues and to form metastases.

Cabazitaxel is a new antineoplastic agent that inhibits the function of microtubules. Like other taxanes, it binds to beta-tubulin and promotes and maintains its incorporation in the assembled microtubule. As a consequence the dynamic structure of the microtubule cytoskeleton is 'frozen' and the concentration of free tubulin decreased. Mitotic cells, which depend on microtubules to restructure their shape and organelle organization, undergo apoptosis or stop pro…