What do you do with an unpredictable protein structure?

You Foldit! Foldit, as in the science-based puzzle game. In my last post, I already talked a little bit about this phenomenal game. I decided to look into it with a more in-depth perspective. I found a scientific journal entry and dared to share my findings. Unfortunately, I must confess that I'm not well-informed with science term lingo, but the main points I want to make about Foldit are still intact.

First, let's recap on what this thing is. In the journal's words it describes Foldit as "a multiplayer online game that enlists players worldwide to solve difficult protein-structure prediction problems" (pg.1). Players have to use all sorts of things like three-dimensional problem solving skills to the use of teammate skills, but thankfully an understanding in molecular biology is not required. The game gives high scores, which depend on the low energy of the protein, and has different tools that allow players to create and predict protein models.

The journal talks about how there are many protein modeling problems that are cooperative to comparative modeling from the structures of homologous or similar proteins. The journal also says that, "To make use of homology modeling techniques in Foldit, we introduced a new capability called the Alignment Tool, which allows players to manually move alignments and thread their sequence onto the structures of known homologs" (pg.1). So, a similar protein is given and it is the players'jobs to find a new protein by making very tiny tweaks here and there, a term referred to by the journal as "tunneling".

The creators of Foldit held a competition in order "to determine whether human intuition could succeed where automated methods had failed, [they] challenged Foldit players to build accurate models of M-PMV PR" (pg.3). The M-PMV PR is an AIDS causing monkey virus. For over a decade, even with several crystallized forms, researchers have been unable to solve the protein structure using several different methods, one of them being model replacement. After only three weeks, when the competition ended, the researchers looked at the top-scorers' models. Several solutions were actually good enough estimates that it allowed a rapid solution for the crystal structure. As the players progressed for a few days, they finally completed a final superior, polished structure.

The last paragraph in the journal sums up the purpose of Foldit ,which goes hand in hand with the blog. It shows the power of online games and how it uses human intuition and three-dimensional pattern-matching skills in order to find a solution to difficult scientific problems. Much attention has been given to game playing potential, but for serious scientific problems this may be the first example of how online gamers can help. Page three, the last page,  gives the final conclusion of the actual potential, "These results indicate the potential for integrating video games into the real-world scientific process: the ingenuity of game players is a formidable force that, if properly directed, can be used to solve a wide range of scientific problems."
Are you excited to know how games can be used for medical and scientific purposes, or do you think this will all blow over and Foldit was simply a unique but not very repeatable idea?
Let's keep playing!


Khatib, F., DeMaio, F., Cooper, S., Kazmireczyk, M., Gilski, M., Kryzwda, S., Zabranska, H.,Thompson, J., Popovic, Z., Jaskolski, M., Pichova, I., & Baker, D. (2011). Crystal structure of a monomeric retroviral protease solved by protein folding game players. Nature Structural and Molecular Biology, 3. Retrieved from http://www.nature.com/nsmb/

The Spectrum of Digital Reality

After reading an interesting article from The Economist, I know now that there are already several uses for video game technology.  To start off my research, I decided to investigate the topics that were discussed in the article more in depth, as well as other related material, and please remember to comment with your thoughts on issues that may be brought up.

The first video game tool mentioned in the article is one you may be familiar with.  It is a driving simulation developed by Code Masters, which can simulate real world cars and circuits in every detail.   Many drivers have already taken advantage of this simulation.  Only research will tell if this has helped drivers improve their skills.  How would you feel if you learn to drive with a video game?

Next on the list is implementing warfare games.  Video game warfare simulations like “Steel Beast” built by eSim games.  Another game “Virtual Battle space 2” has been experimented with training soldiers in countries like Canada, Britain, and Australia. The game was developed by Bohemian Interactive. The author talks about how this can be beneficial because, “If a commander wants his troops to practice infantry combat in the fog, he doesn’t have to wait for the weather to oblige; he can conjure it up on his computer” (p.10). Satellite images can generate virtual substitutes of real places allowing soldiers to rehearse missions and then later analyze the data. Does it make you feel uncomfortable to know how close real war has come to being just a game? If we continue using games for warfare training purposes, could we lose the severity of taking someone’s life?

                Business companies are also being pulled in. Instead of having a classroom setting students can learn to handle life like situations by playing a game.

                In my opinion though, the most innovative way on using games that I’ve heard of is a game called “Foldit”. Thanks to molecular biology we know that “proteins are complicated chemicals made of long chains of amino acids, the tiny chemical building blocks of life. Those chains can fold up in billions of different ways, and the process by which they arrive are poorly understood.”(p.11).These proteins can be misfolded and are implicated to neurological diseases. Computers can recognize a protein folded correctly, but it struggles when it actually has to find the protein.

A team from the University of Washington invented “Foldit”. It is a free online puzzle game that provides players with a task of finding a protein’s most energy efficient shape. The game with its 40, 000 users have made a serious contribution to biology. Seeing as how this game has helped scientists, do you think this avenue should be pursued?

What all this is, is turning what makes video games fun and applying those methods to other activities. This term is called “gamification”. "Gamifiers try to capture that sense of engagement by providing rapid, continuous feedback, a clear sense of progression and goals that are challenging enough to maintain interest but no so hard as to put players off"(pg.11). According to the magazine ther are many who are not convinced because too much gamification doesn't seem to differ in decent management. Well readers, what do you think? Also, be sure to check out the link provided. The video is The Economist interviewing the author, Tim Cross, about the article. The video talks about more video game topics, but if you would like to skip to the part that discusses what my blog is written on skip to 5 minutes and 25 seconds.
Tim Cross, T. C. (2011, December 10). All the world's a game. The Economist, 401(8763), 10-11.
Click here for the link. Enjoy!
Let's keep playing!

Will Video Games Serve Other Purposes Besides Entertainment?

 This a question that I have asked myself plenty of times. I respect the idea that everything evolves, which is coming from someone who sometimes wishes he had an older soul, and I am seeing that video games are becoming more and more in sync to the daily lives of people rather than a small group of kids playing on the weekend. In a way this question can be answered with a hesitant yes, and hesitant because people are not utilizing games on the massive scale of what it could actually become.

  I chose to write about this topic to share information and discuss how or even if video games will progress to areas either outside of entertainment or utilizing the entertainment part for a greater ambition. Even if you aren't into games, although if you love Temple Run or Angry Birds you're playing games, it is a wise decision to learn about subjects that are becoming quite popular. Since the gaming industry, according to PricewaterhouseCoopers, is as of last year worth 56 billion dollars, which is twice the recorded music industry, I would say video games are something to take a peek at. 

  As a gamer when my time allows, this topic should be fun, and I hope that for any reader that it will be pleasing, engaging,and informative.
    Let's keep playing!