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Multivariate analysis of a data matrix containing A‐DNA and B‐DNA dinucleoside monophosphate steps: Multidimensional Ramachandran plots for nucleic acids
Author(s) -
Beckers M. L. M.,
Buydens L. M. C.
Publication year - 1998
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/(sici)1096-987x(199805)19:7<695::aid-jcc2>3.0.co;2-l
Subject(s) - ramachandran plot , singular value decomposition , mathematics , torsion (gastropod) , nucleic acid , dna , biological system , algorithm , chemistry , biology , genetics , biochemistry , protein structure , zoology
A method to construct the equivalent of multidimensional Ramachandran plots for nucleic acids on the basis of singular value decomposition (SVD) is presented. For this purpose, a data matrix containing 244 DNA dinucleoside monophosphate steps, represented by nine torsion angles, was decomposed into a score and loading matrix. It is shown that biplots, containing both score points and loading vectors, provide a simple tool to interpret the principles of DNA class separation. Scores separate the data matrix into one A‐DNA class, two different B‐DNA classes, and one so‐called crankshaft class. Loading vectors correlate torsion angles. The projections of scores on loading vectors indicate which torsion angles play a dominant role in DNA class separation. The results of the biplots are supported by (simple) physical interpretations. From a three‐dimensional score space the nine original torsion angles can be reconstructed. Hence, the potential to create the multidimensional equivalent of a Ramachandran plot is available; that is, forbidden and accessible regions in the reduced space reflect these same regions in the nine‐dimensional original space. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 695–715, 1998