Literature DB >> 3857574

Solution of the embedding problem and decomposition of symmetric matrices.

M J Sippl, H A Scheraga.   

Abstract

A solution of the problem of calculating cartesian coordinates from a matrix of interpoint distances (the embedding problem) is reported. An efficient and numerically stable algorithm for the transformation of distances to coordinates is then obtained. It is shown that the embedding problem is intimately related to the theory of symmetric matrices, since every symmetric matrix is related to a general distance matrix by a one-to-one transformation. Embedding of a distance matrix yields a decomposition of the associated symmetric matrix in the form of a sum over outer products of a linear independent system of coordinate vectors. It is shown that such a decomposition exists for every symmetric matrix and that it is numerically stable. From this decomposition, the rank and the numbers of positive, negative, and zero eigenvalues of the symmetric matrix are obtained directly.

Mesh:

Year:  1985        PMID: 3857574      PMCID: PMC397523          DOI: 10.1073/pnas.82.8.2197

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  3 in total

1.  The Protein Data Bank: a computer-based archival file for macromolecular structures.

Authors:  F C Bernstein; T F Koetzle; G J Williams; E F Meyer; M D Brice; J R Rodgers; O Kennard; T Shimanouchi; M Tasumi
Journal:  J Mol Biol       Date:  1977-05-25       Impact factor: 5.469

2.  Combined use of proton-proton Overhauser enhancements and a distance geometry algorithm for determination of polypeptide conformations. Application to micelle-bound glucagon.

Authors:  W Braun; C Bösch; L R Brown; N Go; K Wüthrich
Journal:  Biochim Biophys Acta       Date:  1981-02-27

3.  Sequential resonance assignments as a basis for determination of spatial protein structures by high resolution proton nuclear magnetic resonance.

Authors:  K Wüthrich; G Wider; G Wagner; W Braun
Journal:  J Mol Biol       Date:  1982-03-05       Impact factor: 5.469

  3 in total
  5 in total

1.  Data smashing: uncovering lurking order in data.

Authors:  Ishanu Chattopadhyay; Hod Lipson
Journal:  J R Soc Interface       Date:  2014-12-06       Impact factor: 4.118

2.  3D genome reconstruction from chromosomal contacts.

Authors:  Annick Lesne; Julien Riposo; Paul Roger; Axel Cournac; Julien Mozziconacci
Journal:  Nat Methods       Date:  2014-09-21       Impact factor: 28.547

3.  An approach to the multiple-minima problem by relaxing dimensionality.

Authors:  E O Purisima; H A Scheraga
Journal:  Proc Natl Acad Sci U S A       Date:  1986-05       Impact factor: 11.205

4.  Cayley-Menger coordinates.

Authors:  M J Sippl; H A Scheraga
Journal:  Proc Natl Acad Sci U S A       Date:  1986-04       Impact factor: 11.205

5.  Distance matrix-based approach to protein structure prediction.

Authors:  Andrzej Kloczkowski; Robert L Jernigan; Zhijun Wu; Guang Song; Lei Yang; Andrzej Kolinski; Piotr Pokarowski
Journal:  J Struct Funct Genomics       Date:  2009-02-18
  5 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.