Recent advances on the interval distance geometry problem

Douglas S. Gonçalves (), Antonio Mucherino (), Carlile Lavor () and Leo Liberti ()
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Douglas S. Gonçalves: Universidade Federal de Santa Catarina
Antonio Mucherino: Université de Rennes 1
Carlile Lavor: University of Campinas (IMECC-UNICAMP)
Leo Liberti: CNRS LIX, École Polytechnique

Journal of Global Optimization, 2017, vol. 69, issue 3, No 1, 525-545

Abstract: Abstract We discuss a discretization-based solution approach for a classic problem in global optimization, namely the distance geometry problem (DGP). We focus our attention on a particular class of the DGP which is concerned with the identification of the conformation of biological molecules. Among the many relevant ideas for the discretization of the DGP in the literature, we identify the most promising ones and address their inherent limitations to application to this class of problems. The result is an improved method for estimating 3D structures of small proteins based only on the knowledge of some distance restraints between pairs of atoms. We present computational results showcasing the usefulness of the new proposed approach. Proteins act on living cells according to their geometric and chemical properties: finding protein conformations can be very useful within the pharmaceutical industry in order to synthesize new drugs.

Keywords: Distance geometry; Discretization; Molecular conformation (search for similar items in EconPapers)
Date: 2017
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Citations: View citations in EconPapers (7)

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DOI: 10.1007/s10898-016-0493-6

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