Combining sequence-based prediction methods and circular dichroism and infrared spectroscopic data to improve protein secondary structure determinations

BMC Bioinformatics
Jonathan G Lees, Robert W Janes

Abstract

A number of sequence-based methods exist for protein secondary structure prediction. Protein secondary structures can also be determined experimentally from circular dichroism, and infrared spectroscopic data using empirical analysis methods. It has been proposed that comparable accuracy can be obtained from sequence-based predictions as from these biophysical measurements. Here we have examined the secondary structure determination accuracies of sequence prediction methods with the empirically determined values from the spectroscopic data on datasets of proteins for which both crystal structures and spectroscopic data are available. In this study we show that the sequence prediction methods have accuracies nearly comparable to those of spectroscopic methods. However, we also demonstrate that combining the spectroscopic and sequences techniques produces significant overall improvements in secondary structure determinations. In addition, combining the extra information content available from synchrotron radiation circular dichroism data with sequence methods also shows improvements. Combining sequence prediction with experimentally determined spectroscopic methods for protein secondary structure content significantly enhances th...Continue Reading

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Citations

May 11, 2010·Quarterly Reviews of Biophysics·B A Wallace

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Methods Mentioned

BETA
sequence-based prediction
sequence based prediction
Seq
circular dichroism

Software Mentioned

PISCES
PSI
EVA
BLAST
DSSP
Threader

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