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


RESULTS
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.


CONCLUSIONS
Combining sequence prediction with experimentally determined spectroscopic methods for protein secondary structure content significantly enhances the accuracy of the overall results obtained.
Lees
Jonathan G
JG
School of Biological and Chemical Sciences, Queen Mary, University of London, London E1 4NS, UK. lees@biochem.ucl.ac.uk
Janes
Robert W
RW
D000465:Algorithms; D000595:Amino Acid Sequence; D002942:Circular Dichroism / Q000379:methods*; D003198:Computer Simulation; D008956:Models, Chemical; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010449:Peptide Mapping / Q000379:methods*; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry* / Q000648:ultrastructure; D020539:Sequence Analysis, Protein / Q000379:methods*; D013055:Spectrophotometry, Infrared / Q000379:methods*; D018511:Systems Integration
D011506:Proteins