Citations and references
What follows are a list of references and citations for the various programs used in the current incarnation of the Jpred service.
A description of the Jpred 3 server has been recently published:
Cole C, Barber JD and Barton GJ. (2008) The Jpred 3 secondary structure prediction server, Nucleic Acids Res. 36 (suppl. 2): W197-W201
[Open Access]
The Jnet secondary structure prediction algorithm was published in:
Cuff, J. A. and Barton, G. J. (2000) Application of Enhanced Multiple Sequence Alignment Profiles to Improve Protein Secondary Structure Prediction, PROTEINS: Structure, Function and Genetics 40:502-511
[Medline][HTML preprint]
The analysis and motivation behind the Jpred server can be found in:
Cuff, J. A. and Barton, G. J. (1999) Evaluation and Improvement of Multiple Sequence Methods for Protein Secondary Structure Prediction, PROTEINS: Structure, Function and Genetics 34:508-519
[Medline][HTML preprint][PDF preprint]
The original Jpred server was published in:
Cuff, J. A., Clamp, M. E., Siddiqui, A. S., Finlay, M. and Barton, G. J. (1998) Jpred: A Consensus Secondary Structure Prediction Server, Bioinformatics 14:892-893
[Medline][HTML preprint][PS preprint][PDF preprint]
The Jpred server is also discussed in the following CCP11 newsletter:
CCP11 Newsletter Issue 6, Vol 2.4 - 17 November 1998
Programs used by the current Jpred service include (in no particular order):
- Altschul, S. F., Madden, T. L., Schäffer, A. A., Zhang, J., Zhang, Z., Miller, W. and Lipman, D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res. 25:3389-3402 [Medline][Homepage]
- Lupas, A., Van Dyke, M. and Stock, J. (1991) Predicting Coiled Coils from Protein Sequences, Science 252:1162-1164 [Medline][Homepage]
- Eddy, S. R. (1998) Profile hidden Markov models, Bioinformatics 14:755-763 [Medline][Homepage]
- Barton, G. J. (1993) ALSCRIPT: a tool to format multiple sequence alignments, Protein Eng. 6:37-40 [Medline][Homepage]
- OC [Homepage]
- Kabsch, W. and Sander, C. (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features, Biopolymers 22:2577-2637 [Medline][Homepage]
- Stuttgart Neural Network Simulator (SNNS) v4.2 [Homepage]