An adaptive bin framework search method for a beta-sheet protein homopolymer model |
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Authors: | Alena Shmygelska Holger H Hoos |
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Institution: | (1) Department of Structural Biology, Stanford University, 299 W. Campus Dr, Stanford, CA 94305, USA;(2) Department of Computer Science, University of British Columbia, 2366 Main Mall, Vancouver, BC V6T 1Z4, Canada |
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Abstract: | Background The problem of protein structure prediction consists of predicting the functional or native structure of a protein given its linear sequence of amino acids. This problem has played a prominent role in the fields of
biomolecular physics and algorithm design for over 50 years. Additionally, its importance increases continually as a result
of an exponential growth over time in the number of known protein sequences in contrast to a linear increase in the number
of determined structures. Our work focuses on the problem of searching an exponentially large space of possible conformations
as efficiently as possible, with the goal of finding a global optimum with respect to a given energy function. This problem
plays an important role in the analysis of systems with complex search landscapes, and particularly in the context of ab initio protein structure prediction. |
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