Bioinformatics—The new home for protein sequence motifs
Executive Editor
Protein domains and sequence motifs have been very influential in the field of molecular biology. These units are the common currency of protein structure and function. The Protein Sequence Motifs series in Trends in Biochemical Sciences was an extremely popular forum to publish these results, but sadly the journal published the final one in 2004 (McEntyre and Gibson 2004).
Bioinformatics is well placed to publish reports of novel protein domains and over the past year we have published reports of the MEDs and PocR domains (Anantharaman and Aravind, 2005), the G5 domain (Bateman et al., 2005), the Why domain (Ciccarelli and Bork 2005) and the OCRE domain (Callebaut and Mornon 2005). In this issue we publish the PilZ domain (pronounced ‘pills’) by Amikam and Galperin (2005). This manuscript strongly suggests that the PilZ domain mediates binding to c-di-GMP a universal bacterial second messenger. Because the PilZ is found in hundreds of bacterial proteins this work will have a large impact in understanding bacteria.
I would like to invite you to submit your next novel domain finding as a Discovery Note to Bioinformatics. We will also consider papers that describe the unification of existing protein families and domains into a larger superfamily. Discovery notes are papers intended for the reporting of biologically interesting discoveries using computational techniques. Discovery notes can be up to 4 journal pages length. The instructions to authors can be found at the following URL: http://www.oxfordjournals.org/bioinformatics/for_authors/general.html
If you would like a quick assessment of your domain discovery please send me a pre-submission enquiry outlining the domain and the biological significance of the finding.
REFERENCES
Amikam, D. and Galperin, M.Y. (2005) PilZ domain is part of the bacterial c-di-GMP binding protein. Bioinformatics, 22, 3–6.
Anantharaman, V. and Aravind, L. (2005) MEDS and PocR are novel domains with a predicted role in sensing simple hydrocarbon derivatives in prokaryotic signal transduction systems. Bioinformatics, 21, 2805–2811
Bateman, A., et al. (2005) The G5 domain: a potential N-acetylglucosamine recognition domain involved in biofilm formation. Bioinformatics, 21, 1301–1303
Callebaut, I. and Mornon, J.P. (2005) OCRE: a novel domain made of imperfect, aromatic-rich octamer repeats. Bioinformatics, 21, 699–702
Ciccarelli, F.D. and Bork, P. (2005) The WHy domain mediates the response to desiccation in plants and bacteria. Bioinformatics, 21, 1304–1307
McEntyre, J.R. and Gibson, T.J. (2004) Patterns and clusters within the PSM column in TiBS, 1992–2004. Trends Biochem Sci, . 29, 627–633[CrossRef][Medline].
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