Foldit!: Protein, DNA and Origami of Life

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Foldit!: Protein, DNA and Origami of life When: Who: Camp runs for one week starting from July 7- Incoming 9th-12th graders August 11; 9AM- 3PM; (M-F) Where: Monday-Thursday: Paul G. Allen Center for Computer Science Engineering, UW Friday: CSNE at 1414 NE 42nd St.; Suite 204; Seattle, WA 98105 What: "FoldIt: Proteins, DNA, and the Origami of Life" is an exciting summer camp where students will explore and learn the science behind the online video game ‘Foldit.’ ‘Foldit’ is an experimental research project developed by UW Center for Game Science and UW Department of Biochemistry which enlists the expertise of online gamers to help scientists solve various relevant “real world” problems. The goal of the game is to fold the proteins in the best way possible. The highest scoring solutions are analyzed by scientists, which can then be applied to the relevant proteins. Through a flexible activity structure, students will participate in collaborative game play and engage in activities that illuminate the connections among bioinformatics, molecular biology, and computer science through the framework of participatory citizen science. Campers will deepen their understanding of protein structure and functioning, as well as key concepts in the life sciences and the ethics of science. Additionally, campers will have an opportunity to network with visiting experts and work with bioinformatics tools like Pymol and Rosetta. Finally, campers will work on a culminating project based on self-chosen interests and compete in a culminating puzzle challenge. As a part of this camp students will tour Center for Sensorimotor and Neuroscience. One of the most exciting experiences for the campers will be playing with the device developed by CSNE students called WrestleBrainia 3000, which harnesses the activation energy in the muscles to power robots to compete. Participants get direct visual feedback about their muscle firing patterns and learn basic concepts about the nervous system and neural engineering. How fun it is to play Wrestlebrania3000 Students at the 2014 Brain Awareness Week event EMG arm-wrestling game trying out gesture recognition camera game Photo Courtesy: CSNE Other experiences might include: • Donning an Emotiv EPOC head set which uses 14 sensors and 2 references to detect electrical signals produced by the brain to control a computer icon using only their thoughts; • Wearing a NeuroSky MindWave headset with biosensors that measures brain and motor signals; • Using CREATIVE gesture recognition camera that allows users to play a video game by manipulating their hand in front of the camera and complementary software programs. .

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Foldit Gamers Improve Protein Design Through Crowdsourcing 25 January 2012, by Bob Yirka
Foldit gamers improve protein design through crowdsourcing 25 January 2012, by Bob Yirka chemical reactions. In earlier versions of the Foldit game, players were simply given existing proteins to play with and asked to find the minimal energy state for them by folding them in optimum ways, this latest version has gone much farther by giving players the opportunity to come up with a whole new protein design. To create the new design, gamers were given a Image: Nature Biotechnology (2012) simple beginning structure and some basic ideas doi:10.1038/nbt.2109 about the goal of the new protein, in this case to serve as a better catalyst for a class of Diels-Alder reactions, which are used to synthesize many commercial products. After offering some ideas (PhysOrg.com) -- Gamers on Foldit have such as remodeling certain sections to make them succeeded in improving the catalyst abilities of an behave in certain ways, the gamers went to work enzyme, making it 18-fold more active than the folding the proteins using the tools at hand. original version. The idea is the brainchild of University of Washington scientist Zoran Popovic The first go-round proved mostly futile, with few who is director of the Center for Game Science, gamers coming up with good improvements. To and biochemist David Baker. Together they have improve the results, the team took the best foldings created the Foldit site which is a video game from the first round and fed them back into the application that allows players to work with protein game allowing gamers to improve on them.
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Algorithm discovery by protein folding game players Firas Khatiba, Seth Cooperb, Michael D. Tykaa, Kefan Xub, Ilya Makedonb, Zoran Popovićb, David Bakera,c,1, and Foldit Players aDepartment of Biochemistry; bDepartment of Computer Science and Engineering; and cHoward Hughes Medical Institute, University of Washington, Box 357370, Seattle, WA 98195 Contributed by David Baker, October 5, 2011 (sent for review June 29, 2011) Foldit is a multiplayer online game in which players collaborate As the players themselves understand their strategies better than and compete to create accurate protein structure models. For spe- anyone, we decided to allow them to codify their algorithms cific hard problems, Foldit player solutions can in some cases out- directly, rather than attempting to automatically learn approxi- perform state-of-the-art computational methods. However, very mations. We augmented standard Foldit play with the ability to little is known about how collaborative gameplay produces these create, edit, share, and rate gameplay macros, referred to as results and whether Foldit player strategies can be formalized and “recipes” within the Foldit game (10). In the game each player structured so that they can be used by computers. To determine has their own “cookbook” of such recipes, from which they can whether high performing player strategies could be collectively invoke a variety of interactive automated strategies. Players can codified, we augmented the Foldit gameplay mechanics with tools share recipes they write with the rest of the Foldit community or for players to encode their folding strategies as “recipes” and to they can choose to keep their creations to themselves. share their recipes with other players, who are able to further mod- In this paper we describe the quite unexpected evolution of ify and redistribute them.
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Three-Dimensional Modeling of Chicken Anemia Virus VP3 and Porcine Circovirus Type 1 VP3 A Major Qualifying Project Submitted to the faculty of WORCESTER POLYTECHNIC INSTITUTE in partial fulfillment of the requirements for the Degree of Bachelor of Science in Biochemistry and Chemistry by: __________________________ Sam Eisenberg __________________________________________ Lee Hermsdorf-Krasin __________________________ Curtis Innamorati September 12th, 2013 Approved: _________________________________ Dr. Destin Heilman, Advisor Department of Chemistry and Biochemistry, WPI Abstract The third viral protein (VP3) of the Chicken Anemia Virus (Apoptin) and Porcine Circovirus Type 1 (PCV1VP3) have potential therapeutic cancer killing properties. Though advances have been made in understanding their apoptotic mechanisms, the reasons behind their cancer cell selectivity have thus far eluded researchers. Further, researchers have been unable to isolate and crystallize these proteins, and this lack of a known structure greatly contributes to the difficulty of studying their selectivity. In the past decade protein prediction algorithms have made great strides in the ability to accurately predict secondary and tertiary structures of proteins. This project aimed to generate possible functional models of these proteins using the available prediction techniques. One significant and well defined function of these proteins is their ability to specifically localize to the cell nucleus or cytoplasm. In order to link and evaluate the results generated from tertiary structure predictions with possible mechanisms for localization, experiments regarding the activity of nuclear export signals in the proteins were performed. The generated models strongly suggest that a conformational change plays a significant role regarding the localization of Apoptin and that the export capabilities of PCV1VP3 are CRM1-dependent.
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