Rigid versus unique determination of protein structures with geometric buildup

DOI10.1007/S11590-007-0060-7zbMath1144.92017OpenAlexW2114469732MaRDI QIDQ941022

Di Wu, Ya-Xiang Yuan, Zhi-jun Wu

Publication date: 4 September 2008

Published in: Optimization Letters (Search for Journal in Brave)

Full work available at URL: https://doi.org/10.1007/s11590-007-0060-7

zbMATH Keywords

distance geometrygraph embeddingbiomolecular modelinglinear and nonlinear systems of equationsprotein structure determinationlinear and nonlinear optimization

Mathematics Subject Classification ID

Biochemistry, molecular biology (92C40) Computational methods for problems pertaining to biology (92-08)

Related Items (16)

The unassigned distance geometry problem ⋮ The interval branch-and-prune algorithm for the discretizable molecular distance geometry problem with inexact distances ⋮ A constrained interval approach to the generalized 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 ⋮ A Branch‐and‐Prune algorithm for the Molecular Distance Geometry Problem ⋮ Hyperbolic smoothing and penalty techniques applied to molecular structure determination ⋮ Solving a generalized distance geometry problem for protein structure determination ⋮ Geometric buildup algorithms for sensor network localization ⋮ Algorithm engineering for optimal alignment of protein structure distance matrices ⋮ Discretization orders for distance geometry problems ⋮ The discretizable molecular distance geometry problem ⋮ On the computation of protein backbones by using artificial backbones of hydrogens ⋮ Euclidean Distance Matrices and Applications ⋮ Molecular distance geometry methods: from continuous to discrete

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• A geometric build-up algorithm for solving the molecular distance geometry problem with sparse distance data
• Some properties for the Euclidean distance matrix and positive semidefinite matrix completion problems
• An updated geometric build-up algorithm for solving the molecular distance geometry problems with sparse distance data
• Solution of the embedding problem and decomposition of symmetric matrices.
• Cayley-Menger coordinates.
• The Molecule Problem: Exploiting Structure in Global Optimization

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