Distance Geometry Optimization for Protein Structures |
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Authors: | Jorge J. Moré Zhijun Wu |
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Affiliation: | (1) Rice University, Houston, Texas, USA |
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Abstract: | We study the performance of the dgsol code for the solution of distance geometry problems with lower and upper bounds on distance constraints. The dgsol code uses only a sparse set of distance constraints, while other algorithms tend to work with a dense set of constraints either by imposing additional bounds or by deducing bounds from the given bounds. Our computational results show that protein structures can be determined by solving a distance geometry problem with dgsol and that the approach based on dgsol is significantly more reliable and efficient than multi-starts with an optimization code. |
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Keywords: | Distance geometry Distance constraints Protein structures |
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