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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.
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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GuitarHero vs Games with Real Instruments
Posted by admin in Learning, Music, Programming on December 9, 2009
For some time now i’ve been interested and have been thinking about learning and video games. When i first played guitarhero a long time ago it was clear to me that, especially with the drum kit, i was actually learning useful hand-foot coordination skills which would pply directly to playing a real drum kit. Unfortunately the guitar was entirely ridiculous (5 button controller) and had nothing to do at all with playing a real guitar except your general body posture. Surely i thought the next step is to have people actually play a guitar. Or a piano for that matter. Why hasn’t anyone made a game like that ? I started playing around with MIDI and OpenGL and made a very rudimentary piano hero kind of game.
But, of course, people have thought of this stuff well before me.
The oldest incarnation of such a thing i found was “Keyboard Mania”, a game developed by Konami in 2000 as an Arcade game. A simple 24-key piano keyboard input device, notes fall from the top, you have to hit them as they reach the bottom.
A much modern version, less of a game and more of a tutor, was until recently called PianoHero (Until Harmonix sent the developer a cease and desist letter) and is now called Synthesia. This is a well written, slick looking program that can be fed with and MIDI file and is totally fun! It was OpenSource until recently but is still free which is fabulous.
Similarily for guitar, people are trying to make gaming software controlled by the actual instrument.The problem here of course is much harder since rather then having a clean stream of input MIDI notes, you have to interpret an audio stream and discern which notes were played. THis is difficult because the the same note can be played in different locations on the guitar especially when multiple notes are played together such as when playing chords.
However, next year a product called Guitar Rising is expected to come out. They seem to have done a pretty good job! These guys have even filed a patent application (pending), quite a broad patent actually which as far as i can tell would include the above piano programs.
A free version of exactly the same concept though is called LittleBigStar or soon to be known as Offbeat, apparently.
Dhani Harrison, the son of Beatle George Harrison, very recently remarked that he’s “working on Rock Band 3 and making the controllers more real so people can actually learn how to play music while playing the game.” He claims: “Give me a couple years, it’s going to happen.” Clearly it’s already happened. But what’s maybe more interesting is that if you read comments and forums about the statement, people are of two minds about that. Many people express a sentiment along the lines of “if i wanted to learn an instrument i’d do it – but i just wanna jam along to my favourite tunes with my friends not having to learn anything complicated”. This is something to think about: Its all good ‘n great to make games or software to teach humans do things more efficiently then was possible before, but they have to want to.
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