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Influence of pruning devices on the solution of molecular distance geometry problems

  • Antonio Mucherino
  • , Carlile Lavor
  • , Therese Malliavin
  • , Leo Liberti
  • , Michael Nilges
  • , Nelson Maculan

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

Abstract

The Molecular Distance Geometry Problem (MDGP) is the problem of finding the conformation of a molecule from inter-atomic distances. In some recent work, we proposed the interval Branch & Prune (iBP) algorithm for solving instances of the MDGP related to protein backbones. This algorithm is based on an artificial ordering given to the atoms of the protein backbones which allows the discretization of the problem, and hence the applicability of the iBP algorithm. This algorithm explores a discrete search domain having the structure of a tree and prunes its infeasible branches by employing suitable pruning devices. In this work, we use information derived from Nuclear Magnetic Resonance (NMR) to conceive and add new pruning devices to the iBP algorithm, and we study their influence on the performances of the algorithm.

Original languageEnglish
Title of host publicationExperimental Algorithms - 10th International Symposium, SEA 2011, Proceedings
PublisherSpringer Verlag
Pages206-217
Number of pages12
ISBN (Print)9783642206610
DOIs
Publication statusPublished - 1 Jan 2011

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume6630 LNCS
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

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