Test problem simulations are presented of the matrix equation, D = BF,
equivalent to least squares data fitting, where the matrices are rectangular
with D and F being experimental data. The chosen application is finding fractions
of secondary structures of proteins from circular dichroism (CD) spectra
employing singular value decomposition, SVD, to obtain the matrix B and its
pseudo- reciprocal. In practice the
first step of the analysis is to select the reduced noise representation of the
CD spectra which sets the bounds for subsequent computation and the development
of the CD noise spectra. The conclusion from analysis is to obtain the
structural component spectra summarizing the database and all the structural
fractions and their uncertainties. The database noise spectrum can be used to
prepare the reduced noise CD spectrum for a new protein to yield its structural
fractions and their uncertainties.
References
[1]
Bevington, P. (1969) Data Reduction and Error Analysis for the Physical
Sciences. McGraw-Hill, New York, 154.
[2]
Forsythe, G.E.,
Malcolm, M.A. and Moler, C.B. (1977) Computer Methods for Mathematical
Computations. Prentice- Hall, Inc., Englewood Cliffs, 192.
[3]
Malinowski, E.R.
(1991) Factor Analysis in Chemistry. 2nd Edition, John Wiley and Sons, New York, 58, 85, 95, 111.
[4]
Olver, P.J. and Shakiban, C. (2006) Applied
Linear Algebra. Pearson Prentice Hall, New Jersey, 425.
[5]
Perrin, C.L. (1970) Mathematics for Chemists.
John Wiley & Sons Inc., New York, 247.
[6]
Press, W.H.,
Flannery, B.P., Teukolsky, S.A. and Vetterling, W.T. (1986) Numerical Recipes.
Cambridge University Press, Cambridge,
52, 60, 172.
[7]
Compton, L.A. and Johnson, W.C. (1986)
Analysis of Protein Circular Dichroism Spectra for Secondary Structure Using a
Simple Matrix Multiplication. Analytical
Biochemistry, 155,
155-167. http://dx.doi.org/10.1016/0003-2697(86)90241-1
[8]
Hennessey, J.P. and Johnson, W.C. (1981) Information Content in the
Circular Dichroism of Proteins. Biochemistry, 20,
1085-1094. http://dx.doi.org/10.1021/bi00508a007
[9]
Hennessey, J.P. and Johnson, W.C. (1982)
Experimental Errors and Their Effect on Analyzing Circular Dichroism Spectra of
Proteins. Analytical Biochemistry, 125,
177-188. http://dx.doi.org/10.1016/0003-2697(82)90400-6
[10]
Miles, A.J.,
Whitmore, L. and Wallace, B.A. (2005) Spectral Magnitude Effects on the
Analyses of Secondary Structure from Circular Dichroism Spectroscopic Data. Protein Science, 14, 368-374. http://dx.doi.org/10.1110/ps.041019905