Wheeler, G. L., Miranda-Saavedra, D. and Barton, G. J. (2008).
"Genome analysis of the unicellular green alga Chlamydomonas reinhardtii indicates an ancient evolutionary origin for key pattern recognition and cell-signaling protein families"
Genetics, 179, 193-7. [Abstract]

Walsh, T. P., Webber, C., Searle, S., Sturrock, S. S. and Barton, G. J. (2008).
"SCANPS: a web server for iterative protein sequence database searching by dynamic programming, with display in a hierarchical SCOP browser."
Nucleic Acids Research, doi: 10.1093/nar/gkn320. [Abstract][FullText][PDF].

SCANPS is a sensitive protein sequence database search tool. It iterates searches in a similar way to PSI-BLAST, but uses full dynamic programming and on-the-fly stastics to improve sensitivity. In benchmarks, SCANPS outperforms PSI-BLAST at identifying remote homologues. The web server includes a novel method of browsing hits to protein domains of known structure that have been organised in the scop hierarchy. You can try the Dundee SCANPS server here. EBI also run a SCANPS server with a different interface. 

Cole, C., Barber, J. D. and Barton, G. J. (2008). 
"The JPRED 3 Secondary structure prediction server",
Nucleic Acids Research, doi: .10.1093/nar/gkn238. [Abstract][FullText][PDF].

This paper describes significant enhancements in accuracy and useability of the JPRED secondary structure prediction server. The new server gives over 80% accuracy for secondary structure prediction in blind tests. Try JPRED 3 here.

Overton, I. M., Johannes van Niekerk, C. A., Carter, L. G., Dawson, A., Martin, D. M. A., Cameron, S., McMahon, S. A.,
White, M. F., Hunter, W. N., Naismith, J. H. and Barton, G. J. (2008)
"TarO: A target optimisation system for structural biology"
Nucleic Acids Research, in press. [Abstract][FullText][PDF].

TarO is a sophisticated protein sequence analysis pipeline that presents the results of orthology searches and many sequence analyses in a concise tabular form and on an annotated multiple sequence alignment displayed in Jalview. Try TarO here and read more about what it does.

Overton, I. M., Padovani, G., Girolami, M. A. and Barton, G. J. (2008)
"ParCrys: A Parzen Window Density Estimation Approach to Protein Crystallisation Propensity Prediction", Bioinformatics, doi:10.1093/bioinformatics/btn055. [Abstract][Advance Access PDF]

Manning, J. R., Jefferson, E. R. and Barton, G. J. (2008), "The contrasting properties of conservation and correlated phylogeny in protein functional residue prediction", BMC Bioinformatics, 9:51.
[Abstract][Provisional PDF]

Jefferson, E. R., Walsh, T. and Barton, G. J., (2008)
"A comparison of SCOP and CATH with respect to domain-domain interactions",
 PROTEINS: Structure, Function and Bioinformatics,
70, 54-62, [Preprint].