Assigned and unassigned distance geometry: applications to biological molecules and nanostructures

DOI10.1007/s10288-016-0314-2zbMath1364.51005DBLPjournals/4or/BillingeDGLM16OpenAlexW2337478696WikidataQ62562129 ScholiaQ62562129MaRDI QIDQ503659

Douglas S. Gonçalves, Simon J. L. Billinge, Antonio Mucherino, Phillip M. Duxbury, Carlile C. Lavor

Publication date: 13 January 2017

Published in: 4OR (Search for Journal in Brave)

Full work available at URL: https://www.osti.gov/biblio/1183260

zbMATH Keywords

distance geometrynanostructuregraph rigiditymolecular conformations

Mathematics Subject Classification ID

Distance geometry (51K99) General theory of distance geometry (51K05) Molecular structure (graph-theoretic methods, methods of differential topology, etc.) (92E10) Classical or axiomatic geometry and physics (51P05) Research exposition (monographs, survey articles) pertaining to biology (92-02) Research exposition (monographs, survey articles) pertaining to geometry (51-02) Statistical mechanics of nanostructures and nanoparticles (82D80)

Related Items (25)

A note on the Cayley-Menger determinant and the molecular distance geometry problem ⋮ Unassigned distance geometry and molecular conformation problems ⋮ Improving the sampling process in the interval branch-and-prune algorithm for the discretizable molecular distance geometry problem ⋮ New upper bounds for the number of embeddings of minimally rigid graphs ⋮ A constrained interval approach to the generalized distance geometry problem ⋮ A NOTE ON COMPUTING THE INTERSECTION OF SPHERES IN ⋮ On the Exact Solution of the Distance Geometry with Interval Distances in Dimension 1 ⋮ Realizing Euclidean distance matrices by sphere intersection ⋮ Minimal NMR distance information for rigidity of protein graphs ⋮ Oriented conformal geometric algebra and the molecular distance geometry problem ⋮ Recent results on assigned and unassigned distance geometry with applications to protein molecules and nanostructures ⋮ NMR protein structure calculation and sphere intersections ⋮ On the estimation of unknown distances for a class of Euclidean distance matrix completion problems with interval data ⋮ On the optimality of finding DMDGP symmetries ⋮ A novel low-rank matrix completion approach to estimate missing entries in Euclidean distance matrix ⋮ Preface: Special issue dedicated to distance geometry ⋮ On the multihomogeneous Bézout bound on the number of embeddings of minimally rigid graphs ⋮ Graph reconstruction from unlabeled edge lengths ⋮ 4OR comes of age. Editorial note ⋮ A new algorithm for the \(^K\)DMDGP subclass of distance geometry problems with exact distances ⋮ Preface ⋮ Global Rigidity of Unit Ball Graphs ⋮ Barvinok's naive algorithm in distance geometry ⋮ On the polynomiality of finding \(^K\text{DMDGP}\) re-orders ⋮ A quantum approach to the discretizable molecular distance geometry problem

Uses Software

• CNS

Cites Work

• Unnamed Item
• Unnamed Item
• Unnamed Item
• Unnamed Item
• Unnamed Item
• The unassigned distance geometry problem
• Discretization orders and efficient computation of Cartesian coordinates for distance geometry
• Discretization orders for protein side chains
• Discretization vertex orders in distance geometry
• On the computation of protein backbones by using artificial backbones of hydrogens
• A linear-time algorithm for solving the molecular distance geometry problem with exact inter-atomic distances
• Discretization orders for distance geometry problems
• The discretizable molecular distance geometry problem
• Clifford algebra and the discretizable molecular distance geometry problem
• Extending the geometric build-up algorithm for the molecular distance geometry problem
• Rigidity of multi-graphs. I: Linking rigid bodies in n-space
• An algorithm for two-dimensional rigidity percolation: The pebble game
• Connected rigidity matroids and unique realizations of graphs
• The discretizable distance geometry problem
• An updated geometric build-up algorithm for solving the molecular distance geometry problems with sparse distance data
• The interval branch-and-prune algorithm for the discretizable molecular distance geometry problem with inexact distances
• On the number of realizations of certain Henneberg graphs arising in protein conformation
• Generic global rigidity
• A point set puzzle revisited
• On graphs and rigidity of plane skeletal structures
• Six mathematical gems from the history of distance geometry
• The Discretizable Molecular Distance Geometry Problem seems Easier on Proteins
• Distance Geometry Methods for Protein Structure Determination
• An Overview on Protein Structure Determination by NMR: Historical and Future Perspectives of the use of Distance Geometry Methods
• Distance Geometry
• Reconstructing a three-dimensional model with arbitrary errors
• WHICH POINT CONFIGURATIONS ARE DETERMINED BY THE DISTRIBUTION OF THEIR PAIRWISE DISTANCES?
• Characterizing generic global rigidity
• On Generic Rigidity in the Plane
• Conditions for Unique Graph Realizations
• An efficient algorithm for testing the generic rigidity of graphs in the plane
• The Molecule Problem: Exploiting Structure in Global Optimization
• Euclidean Distance Geometry and Applications
• On the Identification of Discretization Orders for Distance Geometry with Intervals
• Preface

This page was built for publication: Assigned and unassigned distance geometry: applications to biological molecules and nanostructures