A Protein Secondary Structure Prediction Server

Citations and references

The JPred 4 server is described in NAR (primary JPred citation):
Drozdetskiy A, Cole C, Procter J & Barton GJ. (first published online April 16, 2015) JPred4: a protein secondary structure prediction server, Nucleic Acids Res. Web Server issue
[doi:10.1093/nar/gkv332]
The JPred 4 server was also presented in a poster at ISMB/ECCB conference in Dublin, Jul 2015:
Drozdetskiy A, Cole C, Procter J & Barton GJ. JPred4: a protein secondary structure prediction server, F1000Research 2015, 4(ISCB Comm J):325 (poster):
[doi:10.7490/f1000research.1110063.1]

A description of the JPred 3 server was published in NAR:
Cole C, Barber JD and Barton GJ. (2008) The Jpred 3 secondary structure prediction server, Nucleic Acids Res. 36 (suppl. 2): W197-W201
[PubMed][doi:10.1093/nar/gkn238]

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
[PubMed][doi:10.1002/1097-0134(20000815)40:3<502::AID-PROT170>3.0.CO;2-Q][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
[PubMed][doi:10.1002/(SICI)1097-0134(19990301)34:4<508::AID-PROT10>3.0.CO;2-4][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
[PubMed][doi:10.1093/bioinformatics/14.10.892][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 [PubMed][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 [PubMed][Homepage]
• Stuttgart Neural Network Simulator (SNNS) v4.2 [Homepage]