Postdoctoral Research Fellowships in Biology for FY 2009

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This action funds an NSF Postdoctoral Research Fellowship for FY 2009. The fellowship supports a research and training plan entitled "Automating human intuition to improve protein structure prediction" for Firas Khatib. The host institution for this research is the University of Washington, and the sponsoring scientist is Dr. David Baker.This project uses the combined power of humans and computers to build accurate models of disease-related proteins. Determining the correct structure of a protein helps researchers successfully target them with drugs. Experimental methods for solving proteins are time consuming and expensive, making a computational solution to the protein-folding problem necessary. Even with the current supercomputing and distributed computing power available, new algorithms are needed to solve one of the main computational bottlenecks, conformational sampling. Because a protein chain can have so many different possible conformations, efficient exploration of the search space is crucial. A new approach to this problem is the use of human puzzle-solving intuition and pattern recognition skills combined with computers running Rosetta, the prediction algorithm developed in David Baker's research group. Foldit is an interactive Rosetta-based program allowing users around the world to directly manipulate protein structure models on their home computers in real-time. The ultimate goal of Foldit is to use the results from the computer program to improve structure prediction algorithms by capitalizing on natural human 3D problem-solving skills. The project determines what aspect of the structure prediction problem game-playing humans can improve and implement these new techniques into Rosetta's automated protocol. The successful automation of human intuition would be a remarkable achievement in computational science. Training objectives include development of programming and computational skills as well as teaching and mentoring abilities. Foldit users are able to share their solutions with others around the world, taking advantage of the strengths that different people have, in order to improve results globally. Presentations on Foldit are being given to children and parents at the local science and educational museum and at local high schools in the hope that Foldit could be used in chemistry courses around the world, creating the next generation of protein folders, and then in turn new structure prediction algorithms could be developed based on these new experts' protein-folding skills. This gives worldwide participants an immediate and relevant application for protein-folding knowledge, hopefully reinforcing the motivation to understand the underlying science. In addition, because anyone in the world can contribute to Foldit, this research establishes a global collaborative network. The algorithms and methods developed will be published, and the Rosetta software source code will be freely and openly available to the scientific community.