Unassigned distance geometry and molecular conformation problems

Phil Duxbury (), Carlile Lavor (), Leo Liberti () and Luiz Leduino Salles-Neto ()
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Phil Duxbury: Michigan State University
Carlile Lavor: IMECC-Unicamp
Leo Liberti: CNRS LIX
Luiz Leduino Salles-Neto: Federal University of Sao Paulo

Journal of Global Optimization, 2022, vol. 83, issue 1, No 5, 73-82

Abstract: 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.

Keywords: Unassigned distance geometry problem; Nonlinear optimization; Molecular conformation (search for similar items in EconPapers)
Date: 2022
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DOI: 10.1007/s10898-021-01023-0

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