Dan Rigden.  Selected Publications

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The BACON domain.  By mining metagenomic data from gut bacteria we have found a novel all-β domain with all the hallmarks of a carbohydrate-binding module. It's also in many proteases leading us to suspect that it might often bind to a glycoprotein, perhaps mucin.  The full story is out in FEBS Lett.  We're proud that this work was based on preliminary data obtained by a student on our Masters course in Bioinformatics.

The DxDxDG calcium-binding motif. This motif appears to have evolved many times independently.  I know of no other example of such striking convergent evolution.  This work was published a little while ago in J. Mol. Biol., but Duncan Woodhead, a PhD student shared with Prudence Wong in Computer Science, has contributed to a significant update that in PLoS ONE. 

Sometimes recognising distant homology from non-trivial structure superposition is informative about function.  This example is the unexpected relationship between Erwinia virulence factor and  Bacillus thuringiensis cytolytic toxins, important weapons for production of transgenic pest-resistant crops. Recognising the connection and mapping sequence conservation predicts the location of the lipid binding site in the toxins.  This work is now out in FEBS Lett.

Molecular Replacement with ab initio models.  This BBSRC-funded project has resulted in a program called AMPLE, now released in the CCP4 suite. You can read about it  in the CCP4 newsletter here or get a full description at Acta Cryst D. They kindly let me put the pdf and supplementary here too.

Pex13 is an essential factor for import of proteins into the peroxisome.  The trypanosomatid Pex13 could not be identified by standard BLAST searches.  It's eventual identification rested on the presence of short YG-containing repeats which turn out to be the only conserved factor between Pex13 proteins of different species.  This is out in Biochim. Biophys. Acta.

Pfam contains many Domains of Unknown Function (DUFs).  By combining ab initio modelling with profile-profile matching and non-homology methods, we proposed that many DUFs, encompassing thousands of sequences, act as DNA-binding proteins.  This work is out in OMICS: A Journal of Integrative Biology.

Function annotation of SpoVS.  This protein was characterised as being somehow involved in bacterial sporulation.  Both comparative and ab initio modelling confirmed an Alba-like fold for SpoVS, predicting it to function in controlling gene expression patterns during sporulation.  The full story and GerM analysis were published in Bioinformatics.

Novel MIT domains.  Even the most sensitive PSI-BLAST techniques leave a grey area in searches for the short, sequence diverse MIT domain.  We have found profile-profile matching coupled with ab initio modelling to be highly effective in picking out true MIT domains from among contaminants such as, in this case, the TPR repeat.  More, including experimental validation of one example, in our FEBS Lett. article.

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The contributions of valued collaborators on most of the above are gratefully acknowledged.

Please e-mail me if you can't access these articles from where you are and would like a reprint.