An updated geometric build-up algorithm for solving the molecular distance geometry problems with sparse distance data

DOI10.1007/s10898-006-9080-6zbMath1119.92032OpenAlexW2110543129MaRDI QIDQ2385507

Di Wu, Zhi-jun Wu

Publication date: 12 October 2007

Published in: Journal of Global Optimization (Search for Journal in Brave)

Full work available at URL: https://doi.org/10.1007/s10898-006-9080-6

zbMATH Keywords

Protein structure determinationDistance geometryRoot-mean-square deviation

Mathematics Subject Classification ID

Applications of mathematical programming (90C90) Biochemistry, molecular biology (92C40) Molecular structure (graph-theoretic methods, methods of differential topology, etc.) (92E10)

Related Items (19)

The unassigned distance geometry problem ⋮ The discretizable distance geometry problem ⋮ Recent advances on the discretizable molecular distance geometry problem ⋮ Recent advances on the interval distance geometry problem ⋮ Hyperbolic smoothing and penalty techniques applied to molecular structure determination ⋮ Solving a generalized distance geometry problem for protein structure determination ⋮ Least-squares approximations in geometric buildup for solving distance geometry problems ⋮ A NOTE ON COMPUTING THE INTERSECTION OF SPHERES IN ⋮ Geometric buildup algorithms for sensor network localization ⋮ Recent results on assigned and unassigned distance geometry with applications to protein molecules and nanostructures ⋮ Rigid versus unique determination of protein structures with geometric buildup ⋮ Assigned and unassigned distance geometry: applications to biological molecules and nanostructures ⋮ Discretization orders for distance geometry problems ⋮ The discretizable molecular distance geometry problem ⋮ On the computation of protein backbones by using artificial backbones of hydrogens ⋮ Extending the geometric build-up algorithm for the molecular distance geometry problem ⋮ Euclidean Distance Matrices and Applications ⋮ Molecular distance geometry methods: from continuous to discrete ⋮ A geometric buildup algorithm for the solution of the distance geometry problem using least-squares approximation

Cites Work

• A linear-time algorithm for solving the molecular distance geometry problem with exact inter-atomic distances
• The Solution of the Metric STRESS and SSTRESS Problems in Multidimensional Scaling Using Newtons Method
• A geometric build-up algorithm for solving the molecular distance geometry problem with sparse distance data
• Distance geometry optimization for protein structures
• An Alternating Projection Algorithm for Computing the Nearest Euclidean Distance Matrix
• Global Continuation for Distance Geometry Problems
• The Molecule Problem: Exploiting Structure in Global Optimization
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