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Showing posts from April, 2013

PubMed Watcher - Tailored biomedical literature feed

Following the scientific literature is a difficult task, it's not something you can do lying on the beach. Among the huge number of articles that are published every day only a few really matter to you. These are the articles you are going to have the time to read and that are relevant to your research.

In order to spot the relevant papers, there are a number of thematic approaches. For example, most journals publish articles in a relatively restricted field - and so a scientist can follow a thematic journal (like PLOS, Nature Biotechnology, etc). But then you'll still receive a lot of information to be sorted and you will obviously notice only the recent work. Maybe that interesting article you are waiting for has been published 5 years ago and you will then never ever notice it that way.

You can also keep track of literature with a keywords search (that you save somehow). This approach presents some problems too: What keywords should you search for? Your research is certain…

2nd RDKit UGM, 2-4 October 2013

We are very happy to announce the 2nd RDKit User Group Meeting. The meeting will take place October 2nd-4th here the Genome Campus in Hinxton, UK. We're using a different format for the meeting this year:

Days 1 and 2: Talks, lightning talks, roundtable(s), discussion, and something new: talktorials! Talktorials are somewhere between a talk and a tutorial, they cover something interesting done with the RDKit and include the code used to do the work. During the presentation you'll give an overview of what you did and also show the pieces of the code that are central to the work. The idea is to mix the science up with the tutorial aspects.

Day 3 will be the first ever RDKit sprint: those who choose to stay will spend an intense day working in small groups to produce useful artifacts: new bits of code, knime nodes, knime workflows, tutorials, documentation, IPython notebooks, etc. We'll see who's there and what folks are interested in contributing and go from there.
There wi…

New Drug Approvals 2013 - Pt. V - Canagliflozin (INVOKANA™)

ATC Code: A10BX(incomplete) Wikipedia:Canagliflozin ChEMBL: CHEMBL2048484
On March 29th the FDA approvedCanagliflozin (trade name INVOKANA™) to improve glycemic control for the treatment of diabetes type 2. Canagliflozin is to be used in combination with proper diet and exercise. Canagliflozin is a subtype 2 sodium-glucose transport protein (SGLT2, ChEMBL3884) inhibitor. Canagliflozin is a first-in-class drug with several others still in clinical trials
Target SGLT2 is found in the proximal tubule of the nephron in the kidneys (as is paralog SGLT1, ChEMBL4979). SGLT2 one of the 5 known members of the sodium-glucose transporter proteins family. The transporter is responsible for 90 % of the total renal glucose reuptake (corresponding to 98 % of the uptake in the proximal convoluted tubule). The protein has a relatively low affinity for glucose compared to SGLT1 (2 mM versus 0.4 mM) but a higher capacity. Hence inhibition of this protein leads to a lowering of the glucose plasma concentr…

Book - An introduction to Medicinal Chemistry

There is a new edition of the great med. chem. book "Introduction to Medicinal Chemistry" by Graham Patrick out - I picked up a copy at the Oxford University Press stand at the ACS, and am now flicking through it recovering from the flight from Miami.

Here's a link to the book at Amazon (UK store).


%A G. L. Patrick %T An Introduction To Medicinal Chemistry %D 2013 %I Oxford University Press %O 5th Edition %O ISBN: 978-0-19-969739-7
I worked on some new slides while away, and I think there are a few interesting things to blog about over the next few weeks.

Conference: ICBS2013 - October, Shirankaikan, Japan

The 2013 meeting of the International Chemical Biology Society (ICBS) will be held in Shirankaiken, Japan from October 7th to 9th 2013. Details of the meeting are here.

ChEMBL iPad App from Dotmatics in the iTunes Store

A local SME - Dotmatics - has created a really cool iPad app containing all of ChEMBL 15 in chemically searchable form - chemical structure and property data is local to the iPad, and bioactivity data is then retrieved over the web for selected compounds. Here's a link to details of the app.

New kinase inhibition full matrix dataset

We've just processed and integrated a new full matrix kinase inhibition dataset, kindly provided by EMD Millipore. As described in this recent paper, it covers 234 human wildtype kinases and kinase complexes, as well as 158 'standard' kinase inhibitors tested at two concentrations, leading to more than 73,000 data points. Analysis of the data could provide new insights to kinase selectivity/promiscuity/polypharmacology (depends on how you look at it) and their relationship with chemical structure. The dataset will be available with ChEMBL_16 next month. 
PS: The image above shows the activity profile of four kinase inhibitors across the human kinome families from the Millipore data. It was produced with circos by Rita. 
George