The ChEMBL-og

What / why? As you might know, EMBL-EBI has a very powerful cluster. Yet some time ago we were running into some limitations and were pondering on how great it would be if we had the ability to run more concurrent threads in a single machine (avoiding the bottleneck that inevitably appears on the network for some jobs). It turns out there is an answer, namely in the form of a GPU (graphics processing unit). This is the same type of chip that creates 3D graphics for games in your home PC / laptop. While the capabilities of individual calculation cores are relatively limited on GPUs compared to CPUs, they can have a massive amount of them in order to generate 3D environments at the speeds of 60 frames per second. Schematically it looks like this (CPU left, GPU right): As you can see, the CPU can handle 8 threads concurrently, whereas the GPU can handle 2880 ( see also this great youtube video by the myth busters ). We have all kinds of ideas of calculations we want to run o...

A few days ago, there was this post by Derek Lowe, reviewing a recent paper on magic methyls and their occurrence and impact in medicinal chemistry practice. They're called 'magic' because, although methyls are relatively insignificant in terms of size, polarity or lipophilicity, the addition of one in a compound can  sometimes  have a dramatic impact in its potency - much more that it would be attributed to any simple desolvation effects. More generally, the 'magic methyl' phenomenon pops up in discussions about the validity of the  molecular similarity  principle, descriptors, QSAR - almost everything in the applied Chemoinformatics field - and belongs to the general class of ' activity cliffs '.  Methylation is a chemical transformation, and transformations along with their impact on a property of choice can be easily mined and studied using the so-called Matched Molecular Pairs analysis ( MMPA ). We already have a comprehensive da...

The world is a really small place, as these pictures of the EBI reveal. Many thanks to the photographer Tim Nugent.

Well, it looks like the picture above. Kudos to Tim Nugent for the photography and image processing.

The European Commission and EFPIA (European Federation of Pharmaceutical Industries and Associations) has recently announced the 2nd round of the Innovative Medicines Initiative (IMI) scheme, the amount of funding available is quite substantial, but arguably more important to the research community is the embracing of open data and services, and in particular coordinated pre-competitive activities (there is a lovely recent paper on these sort of activities here , a subscription may be required) %J Nature Rev. Drug Discov. %D 2009 %P 701-708 %T Lowering industry firewalls: pre-competitive informatics initiatives in drug discovery %A Barnes MR %A Harland L %A Foord SM %A Hall MD %A Dix I %A Thomas S %A Williams-Jones BI %A Brouwer CR To quote from the EU Commissioner of Science and Research, Janez Potocnik. "We should see results from this exciting new research mechanism very soon and [...] new innovative medicines should reach European patients faster" To quote from Bi...

A brief link to a developing project under the ESRF Research Infrastructure Roadmap - EU-OPENSCREEN . The basic idea is to develop and establish an underpinning infrastructure in a pan-European setting to allow screening and chemical tool identification for new, therapeutically/commercially unvalidated protein targets. This is a fantastically important project at the current time, both scientifically and economically, so I hope you also are interested in it's progress.