The ChEMBL-og

We are going to speak in the Data Integration and Knowledge Management track at the Bio-IT World (Europe) meeting to be held in the beautiful city of Hannover , Germany, October 5th to 7th 2009. Should be a good meeting...

The ChEMBL caravan will always have a place in our hearts, but now we have an office, and we must move on from the pain. It has some walls and a door, with a nice hook for jackets and coats. It is nice, bijou even, and has bought a smile to all our faces. Most importantly it gives us a place to entertain guests and visitors, so if anyone is in the area, please pop by and have a cup 'o tea and a slice 'o cake. As a sideline, to fund the tea and cakes, we have a nice T-shirt - XXXL only, minimum order 10 pieces if you are interested.

We are going to speak at the 238th ACS National Meeting, Washington, DC, August 16-20, 2009 , on "ChEMBL: Large-scale Mapping of Medicinal Chemistry and Pharmacology Data to Genomes". The Abstract for the talk is: Although the majority of effective therapeutics are small molecules, there is relatively little readily accessible public domain data mapping drugs to their molecular targets. When one considers clinical trial stage, or discovery stage data, the situation deteriorates further. However, this type of data is essential for Chemical Biology experiments, and is crucial for informed target selection in drug discovery. To address this issue, we have built a series of large scale databases, known as ChEMBL, that map small molecule structures to their target genes and also their functional effects. This data also captures a large ammount of human and model organism pharmacological data, systems often used in pre-clinical validation and safety pharmacology testing. A variet...

I am on holiday today - sort of. Went to Borders for a Starbucks (product placement hopefully pays well), and while queuing for my Orange Mocha Frappuccino! , I caught sight of the O'Reilly books ; one stood out from the crowd - Programming Collective Intelligence . It looks a very cool collection of code ( Python ) implementing a whole variety of data analysis/machine learning techniques and routines to build smarter, more responsive and adaptive web 2.0 applications. Skimming the pages while I had my caffeine speedball led me to spend my cash. %A Toby Segaran %T Programming Collective Intelligence %I O'Reilly %D 2007 %O ISBN 978-0596529321

No, this isn't a hotel review, despite the picture above; however since finding this image, I now feel compelled to visit Carlsbad, NM to pose under the sign. Now for the post itself; find below some screenshots for an internal interface for StARlite data developed by our close collaborators at the Institute of Cancer Research in Sutton. This interface for StARlite shows some basic workflow themes that give some ideas as to the potential uses of StARlite 'straight out of the tin'. Several of the views will be incorporated into the EMBL-EBI public web interface ;) Bissan's group is developing an integrated system for cancer chemogenomics, called canSAR . Compound Searching: What would an SAR database be without a compound sketcher and search mechanism. Well here is one, implemented with Marvin , and the Dotmatics Pinpoint cartridge. Compound Browsing: A " Top Trumps " view on compounds is quite a useful paradigm for browsing and selecting compounds f...

Published in 1994 in recognition of the huge influence of Motoo Kimura on the field of theoretical studies on molecular evolution. This is a collection of papers and essays published by Kimura over the period 1955 to 1986. The writing is just truly beautiful, the prose, pace and clarity in the text humbles me as a supposed native English speaker (as this blog so clearly shows!). If you're not interested in the science at all, just buy it for the masterclass of technical writing inside. The theme of the book is around The Neutral Theory , quite a contentious issue in evolution (essentially, this states that the vast majority of observed mutations at a molecular level are not adaptive; now flame me!) This book changed the way I thought about mutation, protein sequence and structure and function. Forever. %T Population Genetics, Molecular Evolution, and The Neutral Theory %A Motoo Kimura %E J.F. Crow %D 1994 %I Chicago %O ISBN: 0-226-43562-8

I came across a nice tabular summary of some existing 'public' 'primary' protein-ligand interaction databases that primarily focus on protein-ligand affinity data (so Ki, Kd, IC50, EC50, etc. ), that I have reproduced below (many thanks to Helena Strömbergsson, from Uppsala University for the data). Name Target Class Focus Approx size BindingDB All ~48,000 PDSP Receptors ~47,000 BRENDA Enzymes ~19,000 BindingMOAD All ~3,500 PDBBind All ~3,500 AffinDB All ~700 PLD All ~500 The comparable number from StARlite (31) are 507,645 (of which 186,370 are better than 100nM) for affinity class end-points. Oh, and we have started a new load.....