On the number of realizations of certain Henneberg graphs arising in protein conformation

DOI10.1016/J.DAM.2013.01.020zbMATH Open1288.05121OpenAlexW2081415437WikidataQ62562148 ScholiaQ62562148MaRDI QIDQ2448906FDOQ2448906

Authors: Leo Liberti, Benoît Masson, Jon Lee, Carlile Lavor, Antonio Mucherino 

Publication date: 5 May 2014

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

Full work available at URL: https://doi.org/10.1016/j.dam.2013.01.020

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zbMATH Keywords

graph rigiditydistance geometrybranch-and-pruneprotein conformationpartial reflection

Mathematics Subject Classification ID

Applications of graph theory (05C90) Protein sequences, DNA sequences (92D20) Distance in graphs (05C12) Signed and weighted graphs (05C22)

Cites Work

• Generic global rigidity
• Title not available (Why is that?)
• Conditions for Unique Graph Realizations
• Title not available (Why is that?)
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• Problems of distance geometry and convex properties of quadratic maps
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• Reconstructing a three-dimensional model with arbitrary errors
• Infinitesimally Rigid Polyhedra. I. Statics of Frameworks
• Infinitesimally Rigid Polyhedra. II: Modified Spherical Frameworks
• Molecular modeling and simulation. An interdisciplinary guide
• Theory of semidefinite programming for sensor network localization
• 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
• On the computation of protein backbones by using artificial backbones of hydrogens
• The discretizable distance geometry problem
• The interval branch-and-prune algorithm for the discretizable molecular distance geometry problem with inexact distances
• Reliable computation of the points of intersection of \(n\) spheres in \({\mathbb{R}}^n\)
• Discretization orders for distance geometry problems
• Molecular distance geometry methods: from continuous to discrete
• On the definition of artificial backbones for the discretizable molecular distance geometry problem
• MD-jeep: an implementation of a branch and prune algorithm for distance geometry problems
• Sphere and dot product representations of graphs
• On the number of solutions of the discretizable molecular distance geometry problem
• Universal Rigidity and Edge Sparsification for Sensor Network Localization
• Rigidity Matroids
• On Products of Euclidean Reflections

Cited In (31)

• An impossible combinatorial counting method in distance geometry
• The number of realizations of a Laman graph
• Oriented conformal geometric algebra and the molecular distance geometry problem
• Realizing Euclidean distance matrices by sphere intersection
• Recent results on assigned and unassigned distance geometry with applications to protein molecules and nanostructures
• On the polynomiality of finding \(^K\text{DMDGP}\) re-orders
• Recent advances on the interval distance geometry problem
• Lower bounds on the number of realizations of rigid graphs
• The \(K\)-discretization and \(K\)-incident graphs for discretizable distance geometry
• A numerical-and-computational study on the impact of using quaternions in the branch-and-prune algorithm for exact discretizable distance geometry problems
• A least-squares approach for discretizable distance geometry problems with inexact distances
• Equivalent realisations of a rigid graph
• Minimal NMR distance information for rigidity of protein graphs
• A constrained interval approach to the generalized distance geometry problem
• Optimal partial discretization orders for discretizable distance geometry
• Distance geometry and data science
• On the maximal number of real embeddings of minimally rigid graphs in \(\mathbb{R}^2,\mathbb{R}^3\) and \(S^2\)
• A quantum approach to the discretizable molecular distance geometry problem
• Geometric algebra to describe the exact discretizable molecular distance geometry problem for an arbitrary dimension
• A new algorithm for the \(^K\mathrm{DMDGP}\) subclass of distance geometry problems with exact distances
• A symmetry-based splitting strategy for discretizable distance geometry problems
• On the optimality of finding DMDGP symmetries
• Discretization vertex orders in distance geometry
• Improving the sampling process in the interval branch-and-prune algorithm for the discretizable molecular distance geometry problem
• Calculating the possible conformations arising from uncertainty in the molecular distance geometry problem using constraint interval analysis
• Distance geometry on the sphere
• Assigned and unassigned distance geometry: applications to biological molecules and nanostructures
• New error measures and methods for realizing protein graphs from distance data
• The referenced vertex ordering problem: theory, applications, and solution methods
• On a relationship between graph realizability and distance matrix completion
• On rigidity and realizability of weighted graphs

Uses Software

• MD-jeep

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