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Distance Geometry Optimization for Protein Structures

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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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Authors and Affiliations

  1. Rice University, Houston, Texas, USA

    Jorge J. Moré & Zhijun Wu

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  1. Jorge J. Moré
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  2. Zhijun Wu
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Moré, J.J., Wu, Z. Distance Geometry Optimization for Protein Structures. Journal of Global Optimization 15, 219–234 (1999). https://doi.org/10.1023/A:1008380219900

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