Calculation of coordinates from incomplete and incorrect distance data

DOI10.1007/BF00944917MaRDI QIDQ1086189zbMATH OpenFDO

Authors J. Schlitter

Publication date 1987

Published in ZAMP. Zeitschrift für angewandte Mathematik und Physik (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1007/BF00944917

zbMATH Keywords

cartesian coordinates from distancesdistance geometrymetric matrixNMRnuclear magnetic resonanceprotein conformationsstable modified Gauss algorithm

Mathematics Subject Classification ID

Orthogonalization in numerical linear algebra (65F25) Computational methods for problems pertaining to biology (92-08) Biophysics (92C05)

Review text

A method has been developed to calculate cartesian coordinates from distances by means of a metric matrix. In contrast to usual methods it requires a minimum of four lines of the distance matrix, i.e. a fraction 8/N of all possible distances when applied to a three-dimensional structure. The factorization of the metric matrix is performed with a stable modified Gauss algorithm. The amount of storage and computing time depends linearly on the number of particles considered. Numerical results were obtained for a system of 58 atoms of a protein and compared with the results from other methods.

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Cites work

• A distance geometry program for determining the structures of small proteins and other macromolecules from nuclear magnetic resonance measurements of intramolecular \({}^ 1H-^ 1H\) proximities in solution
• Solution of the embedding problem and decomposition of symmetric matrices.
• The theory and practice of distance geometry

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• Reconstructing a three-dimensional model with arbitrary errors
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