• New Communications with the New CSD

    Cambridge Structural Database Data and Software Update

    Spring is upon us (at least in the Northern Hemisphere) and with it comes, today, the release of the first 2016 update of the Cambridge Structural Database (CSD). There are new data and updated functionality in the new release, to brighten everything up.

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  • Getting your Compounds in Shape

    & Maria Brandl

    We know that most pharmaceutically relevant compounds bind to their targets in a relaxed conformation. The challenge in discovery is to figure out rapidly which conformations are readily accessible for the molecules we are considering. There is now a new solution to address this based on statistical, rather than just energetic approaches.

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  • CSP Blind Test - Best Ever Results!

    ​One of the most exciting events we hold at the CCDC are our blind tests of crystal structure prediction (CSP) methods. This one turned out to be the best yet. CSP is a really attractive problem as the challenge is beautifully simply to express, but monumentally difficult to solve. Perhaps this is why the entire CSP community comes together every few years, often pooling resources, to have a crack. It’s a wonderful model that could be applied to all sorts of challenges in chemistry and other areas of science.

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  • 2014 - The CCDC’s Truly International Year of Crystallography

    ​“Isn’t every year international for crystallography?”

    That’s a question I was asked, in a somewhat tongue-in-cheek manner, by an American structural chemist (who shall remain nameless) towards the end of 2013, as we discussed events planned for the forthcoming UNESCO International Year of Crystallography (IYCr). She had a point, though, as the year was set to show.

    It is certainly the case that the user communities of the Cambridge Structural Database are spread around the world. We have users in 71 countries, so that’s by no means an idle claim, but the year started with the IYCr fanfare and the aim to spread the word about the value of crystallography. The opening ceremony, in Paris in January, was a grand affair, bringing together scientists, politicians and diplomats from around the world. Juliette Pradon presented from the stage details of our work in the Democratic Republic of Congo. The IYCR roadshow then rolled on throughout 2014, energizing specialists and sparking wider interest through radio interviews, documentaries, feature articles, workshops – for specialists and the public - and many international meetings. I was lucky enough to attend the next IYCr congress in Pakistan, in April, where the CCDC’s Ghazala Sadiq presented on the advances we are making in understanding polymorphism and at the IUCr Congress in Montreal in August, where CCDC members gave several presentations and workshops.

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  • A Bumpy Ride Ahead at the CCDC

    Whilst the rest of the world may be gripped by World Cup fever, there’s a more local sporting drama unfolding here at the CCDC.

    Everyone will be familiar with the annual Cambridge vs Oxford boat race. Since 1829 Cambridge have assailed a clear lead of 81 wins to just 78 (you may be detecting a little bias?). The crews for this race prove their worth throughout the year, including during 'The Bumps' -  races between Cambridge colleges who try to catch and ‘bump’ boats starting slightly ahead. These races are not without their history- they first took place in 1827.
    This year there is keen CCDC interest. As a University of Cambridge Partner Institute we have several students studying for their Ph.Ds with us and the usual bonhomie may be shattered this weekend, as two of them captain rival boats. Florian Roessler will be leading his team of elite Darwin college rowers, with Chris Radoux in charge of his exceptional Sidney Sussex boat.
    The tenuous link to something more crystal-based in this blog is the relationship of atomic bumps to the conformation of rings in crystal structures; the ring conformation is generally adopted to keep the chance of atoms bumping into each other at a minimum. This gives us boats and, of course chairs, from where I’ll be enjoying the races. We could have chosen any of thousands of crystal structures to illustrate this, but this one (CCDC refcode NUXTUW) published in the Chilean Journal of Chemistry does it nicely, with the central ring of the molecule adopting a half-boat/half-chair conformation.
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  • Politics: Not nearly as logical as chemistry

    It seems compulsory at the moment for every blog to mention the death of former British Prime Minister, Baroness Thatcher. Most reports focus on the life and political legacy of Britain’s only female Prime Minister, but of course prior to her life in politics, Thatcher began her career as a chemist.
    As an undergraduate at The University of Oxford, the young Thatcher (then Margaret Roberts) undertook a fourth-year dissertation, in 1946-47, on X-ray crystallography of the antibiotic Gramicidin S. This work was carried out in the research group of Dorothy Hodgkin. Jon Agar gives a super account of the importance of science in shaping her life entitled "Thatcher, Scientist", in an article for Notes and Records of the Royal Society (doi:10.1098/rsnr.2010.0096)
    Research into antibiotics was extremely important at the time, with Hodgkin determining the structure of penicillin in 1945. Thatcher never published a paper on the structure of Gramicidin, a sign perhaps of the challenging nature of the task.  Thatcher herself said in a speech to the merging Chemical Society and The Royal Institute of Chemistry, on becoming an Honorary Fellow in 1979:
    “In my day with her we were working on a molecule called gramicidin S. We thought it was the simplest nuclear protein but it turned out to be one of the most complicated and the structure took 30 years to get out. She did it, I didn't!”
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  • Reaching new heights: Ladderanes in the CSD

    ​With the holiday season finally behind us, the usual routine is returning to work at the CCDC. The CCDC window cleaner, Steve, visited today. Gazing idly though my now clean window at Steve, up his ladder, my mind wandered to ladderanes, a rather unusual group of supramolecular structures containing two or more edge-sharing rings of cyclobutane.

    These molecules were first synthesised for use in the field of molecular design; as these rigid, highly-strained molecules (along with other types of ‘rigid molecular racks’) allowed the exact positioning of various functional groups for the study of electron- and energy-transfer processes.

    These ladder-like molecules soon gained further attention, however, when it was reported in a publication in 2002 (doi:10.1038/nature01128) that nature had got there first. Ladderane-type structures were found in anaerobic ammonium-oxidizing (anammox) marine bacteria. It is suggested ladderane-type lipids help increase the density of a particular anammoxosome membrane to form a barrier against diffusion of toxic molecules, produced as the bacteria derive their energy.

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  • ​CCDC Student Project Wins RSC/MGMS Prize

    Our hearty congratulations go to CCDC Ph.D. student Danny Vatvani, who was one of the three winners of the Kate Burt Prize at the recent Royal Society of Chemistry and Molecular Graphics and Modelling Society Young Modellers Forum, held in London. This is a tremendous achievement for a very bright young scientist.

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  • That time again already? Planning for the 2013 Spring ACS National Meeting

    Deadlines for next year’s Spring ACS National Meeting are fast approaching and we have been making plans for CCDC’s attendance in New Orleans.

    The sheer scale of the ACS National Meetings means there’s always far more going on than you have time for and this meeting looks to be no exception. With sessions covering topics that include “Public Databases Serving the Chemistry Community” (Division of Chemical Information), “Drug Discovery: Chemical and Structural Informatics” and “Materials Science” (Division of Computational Chemistry), there looks to be a lot that is relevant to the CCDC’s activities in drug discovery, crystallography and as a provider of scientific data to the community. We’ll be submitting abstracts to some of these sessions and attending as many as we can.

    A session I’m more intimately involved in is one on “Linking Bioinformatic and Cheminformatic Data” which I am co-organising with John Overington from EMBL-EBI. The linkage of chemical and biological spaces is central to the successful understanding and modulation of biological systems, with applications from drug design, the engineering of new molecules, and chemical safety. Because of the historical separation of biology and chemistry at an academic level, our sense is that there are relatively few scientists trained at the interface between these two areas, and few database resources to support their research. Our aims for this session are to offer a review of current challenges surrounding this interface, and explore applications and new directions in the linking and mining of bio- and cheminformatic data. If you have a talk that might be relevant to this session then abstracts can be submitted up until 15 Oct 2012 via http://abstracts.acs.org (Session Code CINF001).

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  • Welcome!

    I’d like to take this opportunity to welcome you to the new and improved CCDC website. Given the big changes that have been implemented (both in terms of the layout and with the technology behind the scenes) we’ve decided to first launch the new site as this ‘beta-release’. This should give you a chance to get used to the updated look, while still giving you the backup of the site you’ve become familiar with over the past few years. Importantly for us, it also allows you to give us your views and feedback as we continue to develop the site. If you have a few spare minutes, please take a look around the new site and fill in our feedback form (there should be a link to the form from every page), we really are keen to hear what you think.

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