Molecular conformation search by distance matrix perturbations

DOI10.1007/S10910-004-1466-4MaRDI QIDQ2485885zbMATH OpenOpenAlexWikidataFDO

Authors Ioannis Z. Emiris, Theodoros G. Nikitopoulos

Publication date 5 August 2005

Published in Journal of Mathematical Chemistry (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1007/s10910-004-1466-4

zbMATH Keywords

matrix perturbationsingular valuedistance geometrylocal conformation search

Mathematics Subject Classification ID

Eigenvalues, singular values, and eigenvectors (15A18) Numerical computation of eigenvalues and eigenvectors of matrices (65F15) Molecular structure (graph-theoretic methods, methods of differential topology, etc.) (92E10)

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Cites work

• A geometric build-up algorithm for solving the molecular distance geometry problem with sparse distance data
• Computing Most Nearly Rank-Reducing Structured Matrix Perturbations
• Distance geometry optimization for protein structures
• Problems of distance geometry and convex properties of quadratic maps
• Shortest-path problems and molecular conformation
• The Componentwise Distance to the Nearest Singular Matrix
• The Euclidian Distance Matrix Completion Problem
• The best Euclidean fit to a given distance matrix in prescribed dimensions

Cited in

(10)

• Algebraic algorithms for structure determination in biological chemistry
• Euclidean distance matrices and applications
• Reconstructing a three-dimensional model with arbitrary errors
• The embedding problem for predistance matrices
• scientific article; zbMATH DE number 3895768 (Why is no real title available?)
• Molecular alignment as a penalized permutation Procrustes problem
• A Euclidean distance matrix model for protein molecular conformation
• Maxent-stress optimization of 3D biomolecular models
• scientific article; zbMATH DE number 1522763 (Why is no real title available?)
• Distance geometry for realistic molecular conformations

Describes a project that uses

Uses Software

• LAPACK
• Matlab
• Scilab

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