Discretization vertex orders in distance geometry

DOI10.1016/J.DAM.2014.08.035zbMATH Open1321.05029OpenAlexW2017850362WikidataQ62562138 ScholiaQ62562138MaRDI QIDQ499358FDOQ499358

Authors: Andrea Cassioli, Oktay Günlük, Leo Liberti, Carlile Lavor 

Publication date: 30 September 2015

Published in: Discrete Applied Mathematics (Search for Journal in Brave)

Full work available at URL: https://doi.org/10.1016/j.dam.2014.08.035

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zbMATH Keywords

proteinbranch-and-pruneDDGPDMDGPmolecular conformationre-order

Mathematics Subject Classification ID

Graph algorithms (graph-theoretic aspects) (05C85) Combinatorial aspects of finite geometries (05B25) Signed and weighted graphs (05C22)

Cites Work

• Geometric science of information. First international conference, GSI 2013, Paris, France, August 28--30, 2013. Proceedings
• Euclidean distance geometry and applications
• Title not available (Why is that?)
• Distance Geometry
• Title not available (Why is that?)
• Molecular modeling and simulation. An interdisciplinary guide
• Combining variable neighborhood search and estimation of distribution algorithms in the protein side chain placement problem
• A Branch‐and‐Prune algorithm for the Molecular Distance Geometry Problem
• A geometric build-up algorithm for solving the molecular distance geometry problem with sparse distance data
• The discretizable molecular distance geometry problem
• Recent advances on the discretizable molecular distance geometry problem
• The discretizable distance geometry problem
• The interval branch-and-prune algorithm for the discretizable molecular distance geometry problem with inexact distances
• On the Identification of Discretization Orders for Distance Geometry with Intervals
• Discretization orders for distance geometry problems
• Molecular distance geometry methods: from continuous to discrete
• On the number of realizations of certain Henneberg graphs arising in protein conformation
• The discretizable molecular distance geometry problem seems easier on proteins
• Counting the Number of Solutions of KDMDGP Instances

Cited In (32)

• An impossible combinatorial counting method in distance geometry
• On the estimation of unknown distances for a class of Euclidean distance matrix completion problems with interval data
• Oriented conformal geometric algebra and the molecular distance geometry problem
• On the polynomiality of finding \(^K\text{DMDGP}\) re-orders
• Recent advances on the interval distance geometry problem
• Integer Programming, Constraint Programming, and Hybrid Decomposition Approaches to Discretizable Distance Geometry Problems
• Constraint programming approaches for the discretizable molecular distance geometry problem
• The \(K\)-discretization and \(K\)-incident graphs for discretizable distance geometry
• NMR protein structure calculation and sphere intersections
• A least-squares approach for discretizable distance geometry problems with inexact distances
• Minimal NMR distance information for rigidity of protein graphs
• On distance-preserving elimination orderings in graphs: complexity and algorithms
• A constrained interval approach to the generalized distance geometry problem
• Preface
• Optimal partial discretization orders for discretizable distance geometry
• A quantum approach to the discretizable molecular distance geometry problem
• Unassigned distance geometry and molecular conformation problems
• Optimal Discretization Orders for Distance Geometry: A Theoretical Standpoint
• A new algorithm for the \(^K\mathrm{DMDGP}\) subclass of distance geometry problems with exact distances
• A note on the Cayley-Menger determinant and the molecular distance geometry problem
• On the optimality of finding DMDGP symmetries
• On the Identification of Discretization Orders for Distance Geometry with Intervals
• Discretization orders and efficient computation of Cartesian coordinates for distance geometry
• Discretization orders for distance geometry problems
• Improving the sampling process in the interval branch-and-prune algorithm for the discretizable molecular distance geometry problem
• Assigned and unassigned distance geometry: applications to biological molecules and nanostructures
• Clifford algebra and the discretizable molecular distance geometry problem
• Tuning interval branch-and-prune for protein structure determination
• New error measures and methods for realizing protein graphs from distance data
• The referenced vertex ordering problem: theory, applications, and solution methods
• An integer programming approach for the search of discretization orders in distance geometry problems
• Geometric algebra to model uncertainties in the discretizable molecular distance geometry problem

Uses Software

• AMPL
• CPLEX

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