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    Knowledge-based environment potentials for protein structure prediction

    Durham, Elizabeth Ashley
    : https://etd.library.vanderbilt.edu/etd-05282008-161200
    http://hdl.handle.net/1803/12412
    : 2008-06-06

    Abstract

    This Master’s Thesis project had as its objectives: (1) to optimize algorithms for solvent-accessible surface area (SASA) approximation to develop an environment free energy knowledge-based potential; and, (2) to assess the knowledge-based environment free energy potentials for de novo protein structure prediction. This project achieved its goals by developing, implementing, optimizing, and evaluating four different algorithms for approximating the SASA of a given protein model and generating knowledge-based potentials for de novo protein structure prediction. The algorithms are entitled Neighbor Count, Neighbor Vector, Artificial Neural Network, and Overlapping Spheres.
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