Cuff, J. A. and Barton, G. J. (2000), "Application of Multiple Sequence Alignment Profiles to Improve Protein Secondary Structure Prediction", PROTEINS:
Structure Function and Genetics, 40:502-511. [PubMed] (EBI)
This paper describes the JNet secondary structure prediction algorithm. JNet gives over 76% accuracy in a comprehensive blind test and also predicts burial of residues and assigns confidence levels to
predictions. The JNet software is available for free download from the JNet pages and is now the default algorithm for the JPred prediction server.
Cuff, J. A. Birney, E., Clamp, M. E. and Barton, G. J. (2000),
"ProtEST: Protein Multiple Sequence Alignments from Expressed Sequence Tags", Bioinformatics, 16, 111-116. [PubMed] [PDF] (EBI)