A New Algorithm for the KDMDGP Subclass of Distance Geometry Problems with Exact Distances

The fundamental inverse problem in distance geometry is the one of finding positions from inter-point distances. The Discretizable Molecular Distance Geometry Problem (DMDGP) is a subclass of the Distance Geometry Problem (DGP) whose search space can be discretized and represented by a binary tree,...

Ausführliche Beschreibung

Gespeichert in:
Bibliographische Detailangaben
Veröffentlicht in:Algorithmica 2021, Vol.83 (8), p.2400-2426
Hauptverfasser: Gonçalves, Douglas S., Lavor, Carlile, Liberti, Leo, Souza, Michael
Format: Artikel
Sprache:eng
Schlagworte:
Online-Zugang:Volltext
Tags: Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
Beschreibung
Zusammenfassung:The fundamental inverse problem in distance geometry is the one of finding positions from inter-point distances. The Discretizable Molecular Distance Geometry Problem (DMDGP) is a subclass of the Distance Geometry Problem (DGP) whose search space can be discretized and represented by a binary tree, which can be explored by a Branch-and-Prune (BP) algorithm. It turns out that this combinatorial search space possesses many interesting symmetry properties that were studied in the last decade. In this paper, we present a new algorithm for this subclass of the DGP, which exploits DMDGP symmetries more effectively than its predecessors. Computational results show that the speedup, with respect to the classic BP algorithm, is considerable for sparse DMDGP instances related to protein conformation.
ISSN:0178-4617
1432-0541
DOI:10.1007/s00453-021-00835-6