Extending the geometric build-up algorithm for the molecular distance geometry problem

DOI10.1016/J.IPL.2008.05.009MaRDI QIDQ975461zbMATH OpenOpenAlexWikidataFDO

Authors Ricardo dos Santos Carvalho, Carlile Lavor, Fábio Protti

Publication date 9 June 2010

Published in Information Processing Letters (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1016/j.ipl.2008.05.009

zbMATH Keywords

algorithmscomputational biologymolecular distance geometry problemNMR spectroscopygeometric build-up algorithm

Mathematics Subject Classification ID

Computer graphics; computational geometry (digital and algorithmic aspects) (68U05)

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Cites work

• scientific article; zbMATH DE number 4213315 (Why is no real title available?)
• A geometric build-up algorithm for solving the molecular distance geometry problem with sparse distance data
• A linear-time algorithm for solving the molecular distance geometry problem with exact inter-atomic distances
• An updated geometric build-up algorithm for solving the molecular distance geometry problems with sparse distance data
• Computational Experience with the Molecular Distance Geometry Problem
• Distance geometry optimization for protein structures
• Global Continuation for Distance Geometry Problems
• Large-Scale Molecular Optimization from Distance Matrices by a D.C. Optimization Approach
• Molecular Modeling of Proteins and Mathematical Prediction of Protein Structure
• Optimization in computational chemistry and molecular biology. Local and global approaches. Conference, Princeton Univ., Princeton, NJ, USA, May 7--9, 1999
• Reliable computation of the points of intersection of \(n\) spheres in \({\mathbb{R}}^n\)
• Solving large scale molecular distance geometry problems by a smoothing technique via the Gaussian transform and D.C. programming
• The Molecule Problem: Exploiting Structure in Global Optimization

Cited in

(28)

• Recent results on assigned and unassigned distance geometry with applications to protein molecules and nanostructures
• The interval branch-and-prune algorithm for the discretizable molecular distance geometry problem with inexact distances
• Double variable neighbourhood search with smoothing for the molecular distance geometry problem
• Hyperbolic smoothing and penalty techniques applied to molecular structure determination
• On the polynomiality of finding \(^K\text{DMDGP}\) re-orders
• A linear-time algorithm for solving the molecular distance geometry problem with exact inter-atomic distances
• The discretizable molecular distance geometry problem
• NMR protein structure calculation and sphere intersections
• Minimal NMR distance information for rigidity of protein graphs
• On the computation of protein backbones by using artificial backbones of hydrogens
• Molecular distance geometry methods: from continuous to discrete
• A constrained interval approach to the generalized distance geometry problem
• A geometric build-up algorithm for solving the molecular distance geometry problem with sparse distance data
• A quantum approach to the discretizable molecular distance geometry problem
• A note on the Cayley-Menger determinant and the molecular distance geometry problem
• An updated geometric build-up algorithm for solving the molecular distance geometry problems with sparse distance data
• On the optimality of finding DMDGP symmetries
• Discretization orders for distance geometry problems
• Least-squares approximations in geometric buildup for solving distance geometry problems
• Calculating the possible conformations arising from uncertainty in the molecular distance geometry problem using constraint interval analysis
• Improving the sampling process in the interval branch-and-prune algorithm for the discretizable molecular distance geometry problem
• Solving Molecular Distance Geometry Problems Using a Continuous Optimization Approach
• Euclidean distance matrices and applications
• Assigned and unassigned distance geometry: applications to biological molecules and nanostructures
• Recent advances on the discretizable molecular distance geometry problem
• Maxent-stress optimization of 3D biomolecular models
• On generating instances for the modular distance geometry problem
• The discretizable distance geometry problem

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