Posts Tagged ‘protein structure’

Protein Breathing Plays Critical Role in Neurodegenerative Disease

 :: Posted by American Biotechnologist on 12-04-2012

Crowdsourcing as a model for protein structure discovery

 :: Posted by American Biotechnologist on 01-13-2011

Protein structure research often involves running complex algorithms on massive supercomputers buried deep within the bowels of some of the nations top academic institutions. Such initiatives are expensive to run and require a significant amount of financial capital and technical support. In order to defray the cost of protein structure research, scientists have come with several alternative methods to supercomputing which ultimately result in faster time to results at a fraction of the cost of supercomputing.

One such technique , which we have discussed in the past (see Foldit! Guilt-Free Computer Gaming for Protein Scientists), was adapted from the world of crowdsourcing and involves tapping in on the brainpower of thousands of individuals from around the world to solve the puzzle of numerous protein structures in an interactive, online gaming platform. At the same time, these individuals are helping refine algorithms used by protein folding software enabling them to become more efficient at solving structural proteomic problems.

[email protected] is another interesting initiative that began around a decade ago by scientists in the Pande Lab at Stanford University. According to the project’s website, [email protected] is a distributed computing project — people from throughout the world download and run software to band together to make one of the largest supercomputers in the world. [email protected] uses novel computational methods coupled to distributed computing, to simulate problems millions of times more challenging than previously achieved.

The project requests that owners of personal computers download the [email protected] software which will allow the [email protected] algorithm to be run on the owner’s local processor. The data will then be fed back to the [email protected] database allowing for many protein folding simulations to be run simultaneously thereby exponentially increasing the amount of daily data added to the publicly available protein structure database.

For more information on the [email protected] project visit

Foldit! Guilt-Free Computer Gaming for Protein Scientists

 :: Posted by American Biotechnologist on 08-10-2010

Do you ever feel guilty that you’ve wasted time playing computer games while you could have been doing something more productive? Perhaps instead of online car racing or shooting up virtual enemies you could have been completing household chores, keeping up to date with progress in your area of research or making headway with that paper you’ve been working on.

Or perhaps you could have been contributing to the field of proteomics by helping solve protein structures! If you like computer games but hate the pangs of guilt that come with it, foldit is the game for you.

Biochemists and computer scientists at the University of Washington two years ago launched an ambitious project harnessing the brainpower of computer gamers to solve medical problems.

The game, Foldit, turns one of the hardest problems in molecular biology into a game a bit reminiscent of Tetris. Thousands of people have now played a game that asks them to fold a protein rather than stack colored blocks or rescue a princess.

Players are given a real amino acid sequence and are asked to fold it into the most appropriate structure that uses the least amount of structural energy. As players proceed with the 3-D puzzle, parts of the protein structure with high structural energy are highlighted in red, prompting the player to try a different configuration. Points are awarded based on how close the protein structure comes to the ideal configuration.

Besides finding new protein structures, Foldit players are helping refine algorithms used by protein folding software enabling them to become more efficient at solving structural proteomic problems.

Foldit’s inventor Seth Cooper and his team recently published a paper in Nature entitled “predicting protein structures with a multiplayer online game.” I tried checking out the website the day the paper was released but traffic to the site following the paper’s publication and associated press coverage crashed foldit’s servers. Foldit has since published an explanation of what happened and assures all wannabe structural biologists that the game is back online with all of its original functionality.