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Our FoldIt Paper is out in PNAS!
Algorithm discovery by protein folding game players
Abstract:
Foldit is a multiplayer online game in which players collaborate and compete to create accurate protein structure models. For specific hard problems, Foldit player solutions can in some cases outperform state-of-the-art computational methods. However, very little is known about how collaborative gameplay produces these results and whether Foldit player strategies can be formalized and structured so that they can be used by computers. To determine whether high performing player strategies could be collectively codified, we augmented the Foldit gameplay mechanics with tools for players to encode their folding strategies as “recipes” and to share their recipes with other players, who are able to further modify and redistribute them. Here we describe the rapid social evolution of player-developed folding algorithms that took place in the year following the introduction of these tools. Players developed over 5,400 different recipes, both by creating new algorithms and by modifying and recombining successful recipes developed by other players. The most successful recipes rapidly spread through the Foldit player population, and two of the recipes became particularly dominant. Examination of the algorithms encoded in these two recipes revealed a striking similarity to an unpublished algorithm developed by scientists over the same period. Benchmark calculations show that the new algorithm independently discovered by scientists and by Foldit players outperforms previously published methods. Thus, online scientific game frameworks have the potential not only to solve hard scientific problems, but also to discover and formalize effective new strategies and algorithms.
Beautiful Proteins in Positively Aware!
I few months back i got a request for a bunch of renderings of HIV proteins for a non-profit magazine called Positively Aware! Now they’ve been printed 
TIG Welding Proteins
Today I swapped my MIG Welder for Kevin’s TIG welder (temporarily) and experimented with TIGing copper together. Turns out its not that hard except that the copper i’m welding is so thin that its really easy to just blow a hole in it or turn it all into a molten puddle with just a little bit too much heat. I found in the end that keeping the electrode tip fairly close but giving lots of power gives a small controllable puddle as opposed to less power and larger distance which gives a much wider puddle. We’ll see if the joints are any good once i start bending and “folding” the whole thing into shape. If they crack then i have screwed it up. I realized after welding all the parts to gether that I should have ground down the excess weld each time piece by piece rather then ding it now with all pieces attached to eachother which is much more unwieldy. And bending the loop regions into their approximate shapes is totally pointless. Might as well leave them straight (just cut to the right length at 1″/aa and bend them later in the context of the secondary structure elements. Steep learning curve but super fun. WIth the TIG too – it’s really fun and clearly a lot more practice needed but it feels really satisfying. MIGing is just metal hot glue. TIGing is so much more precise. And its lovely and quiet and looks gorgeous under the helmet – you can literally see the stream of electrons flying into the base metal like a glowing shower – not like tig where its all splatter and noise and smoke. TIG is clearly the high-class of welding .
Doubt on the common assertion that humans are naturally aggressive
Robert Sapolsky’s study of a baboon tribe which was transformation from a violent patriarchic, warnongering tribe (like humans) into a peaceful, almost egalitarian and stable society is one of the more fascinating demonstration that the ubiquitous assumtions that humnas are “naturally” violent is unlikely true.
An excellent podcast on the matter is here:
An two articles by Sapolsky:
http://www.sharpbrains.com/blog/2008/04/05/peace-among-primates-by-robert-sapolsky/
http://www.sharpbrains.com/blog/2008/04/12/peace-among-primates-part-2/
Robert M. Sapolsky, Ph.D., is the John A. and Cynthia Fry Gunn Professor of Biological Sciences and a professor of neurology and neurological sciences at Stanford University.
Alternate States of Proteins Revealed by Detailed Energy Landscape Mapping
Posted by admin in Programming, Science on December 10, 2010
After about 2 years of work, millions of CPU hours donated by volunteers from around the globe on Rosetta@HOME and a fruitful collaboration with Daniel Keedy and Jane and David Richardson at Duke University our paper on energy landscapes is finally out! Thank you to everyone who helped and especially to Daniel Keedy @ Duke and all who have donated computing time!
Alternate States of Proteins Revealed by Detailed Energy Landscape Mapping
Michael D. Tyka†, Daniel A. Keedy†, Ingemar André, Frank DiMaio, Yifan Song, David C. Richardson, Jane S. Richardson and David Baker
†contributed equally
What conformations do protein molecules populate in solution? Crystallography provides a high-resolution description of protein structure in the crystal environment, while NMR describes structure in solution but using less data. NMR structures display more variability, but is this because crystal contacts are absent or because of fewer data constraints? Here we report unexpected insight into this issue obtained through analysis of detailed protein energy landscapes generated by large-scale, native-enhanced sampling of conformational space with Rosetta@home for 111 protein domains. In the absence of tightly associating binding partners or ligands, the lowest-energy Rosetta models were nearly all < 2.5 Å CαRMSD from the experimental structure; this result demonstrates that structure prediction accuracy for globular proteins is limited mainly by the ability to sample close to the native structure. While the lowest-energy models are similar to deposited structures, they are not identical; the largest deviations are most often in regions involved in ligand, quaternary, or crystal contacts. For ligand binding proteins, the low energy models may resemble the apo structures, and for oligomeric proteins, the monomeric assembly intermediates. The deviations between the low energy models and crystal structures largely disappear when landscapes are computed in the context of the crystal lattice or multimer. The computed low-energy ensembles, with tight crystal-structure-like packing in the core, but more NMR-structure-like variability in loops, may in some cases resemble the native state ensembles of proteins better than individual crystal or NMR structures, and can suggest experimentally testable hypotheses relating alternative states and structural heterogeneity to function.
Alan Turing
Friday I saw an intensely moving and fascinating play on the life and work of Alan Turing (Breaking the Code, written 1986 play by Hugh Whitemore; produced by Strawberry Theatre Workshop; Thu/Fri/Sat 7.30pm @ Erickson Theatre, Seattle). Many years after Turnings work on the Enigma which may well have determined the outcome of the war against Nazi Germany, he was prosecuted by the Governement for his homosexuality and sentenced to chemical sterilization – two year later he commited suicide.
How ironic how often those who fight for freedom against the inhumane oppressors end up being the oppressors and persecutors themselves.
It is sickening how persecution of minority groups continues into so very recent history and to this day. Apparently we have learned nothing. Hey human race, can we please get over this ?
I looked up the official apology issued in 2009 by Prime Minister Gordon Brown on behalf of the UK government:
2009 has been a year of deep reflection – a chance for Britain, as a nation, to commemorate the profound debts we owe to those who came before. A unique combination of anniversaries and events have stirred in us that sense of pride and gratitude which characterise the British experience. Earlier this year I stood with Presidents Sarkozy and Obama to honour the service and the sacrifice of the heroes who stormed the beaches of Normandy 65 years ago. And just last week, we marked the 70 years which have passed since the British government declared its willingness to take up arms against Fascism and declared the outbreak of World War Two. So I am both pleased and proud that, thanks to a coalition of computer scientists, historians and LGBT activists, we have this year a chance to mark and celebrate another contribution to Britain’s fight against the darkness of dictatorship; that of code-breaker Alan Turing.
Turing was a quite brilliant mathematician, most famous for his work on breaking the German Enigma codes. It is no exaggeration to say that, without his outstanding contribution, the history of World War Two could well have been very different. He truly was one of those individuals we can point to whose unique contribution helped to turn the tide of war. The debt of gratitude he is owed makes it all the more horrifying, therefore, that he was treated so inhumanely. In 1952, he was convicted of ‘gross indecency’ – in effect, tried for being gay. His sentence – and he was faced with the miserable choice of this or prison – was chemical castration by a series of injections of female hormones. He took his own life just two years later.
Thousands of people have come together to demand justice for Alan Turing and recognition of the appalling way he was treated. While Turing was dealt with under the law of the time and we can’t put the clock back, his treatment was of course utterly unfair and I am pleased to have the chance to say how deeply sorry I and we all are for what happened to him. Alan and the many thousands of other gay men who were convicted as he was convicted under homophobic laws were treated terribly. Over the years millions more lived in fear of conviction.
I am proud that those days are gone and that in the last 12 years this government has done so much to make life fairer and more equal for our LGBT community. This recognition of Alan’s status as one of Britain’s most famous victims of homophobia is another step towards equality and long overdue.
But even more than that, Alan deserves recognition for his contribution to humankind. For those of us born after 1945, into a Europe which is united, democratic and at peace, it is hard to imagine that our continent was once the theatre of mankind’s darkest hour. It is difficult to believe that in living memory, people could become so consumed by hate – by anti-Semitism, by homophobia, by xenophobia and other murderous prejudices – that the gas chambers and crematoria became a piece of the European landscape as surely as the galleries and universities and concert halls which had marked out the European civilisation for hundreds of years. It is thanks to men and women who were totally committed to fighting fascism, people like Alan Turing, that the horrors of the Holocaust and of total war are part of Europe’s history and not Europe’s present.
So on behalf of the British government, and all those who live freely thanks to Alan’s work I am very proud to say: we’re sorry, you deserved so much better.
Gordon Brown
Beautiful proteins
I started a new blog: http://beautifulproteins.blogspot.com/ . For a while now i’ve been collection PDBs of proteins that i come opon through my work that i find beautiful for some reason. I’ve decided to post some of them to a blog called Beautiful Proteins. Example: Neurotrophin (NGF, Nerve Growth Factor):
100 Most Frequent Internet Search Terms
I’ve been tinkering around, trying to find out what are the most popular searchterms typed into google these days ? Google Trends offers a wealth of data, as do other sites and Meta crawlers and analysis sites. Most published analyses omit adult terms while others (such as Zeitgeist published by Google) concentrate on terms whose search volume is rising quickly compared to their long-term average volume. I feel its insightful to also look at more absolute values though. So here’s a list of the most popular terms I could find: (note this list is approximate and not necessarily complete, nor is the ordering super accurate. The first 10 are fairly accurate though.)
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