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Unassigned distance geometry and molecular conformation problems

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Abstract

3D protein structures and nanostructures can be obtained by exploiting distance information provided by experimental techniques, such as nuclear magnetic resonance and the pair distribution function method. These are examples of instances of the unassigned distance geometry problem (uDGP), where the aim is to calculate the position of some points using a list of associated distance values not previoulsy assigned to the pair of points. We propose new mathematical programming formulations and a new heuristic to solve the uDGP related to molecular structure calculations. In addition to theoretical results, computational experiments are also provided.

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Acknowledgements

We would like to thank the Brazilian research agencies CNPq and FAPESP, for their financial support, and the reviewers for their valuable comments.

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Authors and Affiliations

  1. Michigan State University, Natural Science Building, 288 Farm Lane, East Lansing, MI, USA

    Phil Duxbury

  2. IMECC-Unicamp, Cidade Universitaria Zeferino Vaz, Campinas, Brazil

    Carlile Lavor

  3. CNRS LIX, Ecole Polytechnique, 91128, Palaiseau, France

    Leo Liberti

  4. Science and Technology Institute, Federal University of Sao Paulo, Sao Jose dos Campos, Brazil

    Luiz Leduino de Salles-Neto

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  1. Phil Duxbury
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  2. Carlile Lavor
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  3. Leo Liberti
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  4. Luiz Leduino de Salles-Neto
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Correspondence to Luiz Leduino de Salles-Neto.

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Fapesp and CNPq-Brazil.

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Duxbury, P., Lavor, C., Liberti, L. et al. Unassigned distance geometry and molecular conformation problems. J Glob Optim 83, 73–82 (2022). https://doi.org/10.1007/s10898-021-01023-0

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  • DOI: https://doi.org/10.1007/s10898-021-01023-0

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