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Editor's note - SAS studies in BMC Structural Biology (Simon Harold PhD, 30 May 2012)

Readers may be interested to know that this is the first in a series of articles due to be published in BMC Structural Biology related to structure determination using techniques in Small-Angle Scattering.

You can read about further details of this on our blog: BMC Structural Biology gets some SAXS appeal

Simon Harold PhD
Executive Editor
BMC Structural Biology read full comment

Comment on: Jacques et al. BMC Structural Biology, 12:9

Chosen DNA sequence (Francisco Blanco, 26 October 2010)

I was not able to find in the text (or to track back in the references) the choice of the particular nucleotide sequence of the DNA duplex used to crystallize the complexes of both yeast PCNA (this work) and E coli beta-clamp (reported in Cell. 2008 Jan 11;132(1):43-54.).
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Comment on: McNally et al. BMC Structural Biology, 10:3

Open source tools to repeat this work (Dan Bolser, 19 August 2010)

Much of the software infrastructure used to perform this study has been released in the form of an open source project, hosted at Bioinformatics.Org.

The project's page is here:
The Otto Warburg Java Library For Structural Bioinformatics.

Links to the SVN software repository and the developer mailing list can be found here:
Bioinformatics.Org News & Commentary.
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Comment on: Bolser et al. BMC Structural Biology, 8:53

abstract correction (Chiara Parravicini, 20 May 2010)

Please note that the abstract contains a nonsense in the Conclusions section that should correctly read as follows:

Conclusions: These data thus suggest that, in contrast to what has been hypothesized for nucleotides, the lack of the R255 residue doesn't affect the binding of pranlukast. Aromatic interactions are instead likely to play a predominant role in the recognition of pranlukast, suggesting that two different binding subsites are present on GPR17. read full comment

Comment on: Parravicini et al. BMC Structural Biology, 10:8

An additional reference (Dan Bolser, 12 January 2010)

I was involved in a similar study that may be of interest to readers of the present article. The work included a detailed introduction to the field of empirical potentials as well as a comparison of a 'partner number' type score to a more conventional pairwise empirical potential.


Details:

Residue contact-count potentials are as effective as residue-residue contact-type potentials for ranking protein decoys. Bolser DM, Filippis I, Stehr H, Duarte J, Lappe M. BMC Structural Biology 2008, 8:53 doi:10.1186/1472-6807-8-53

http://www.biomedcentral.com/1472-6807/8/53


* A similar comment has been posted against that article on the BMC website. read full comment

Comment on: Bahadur et al. BMC Structural Biology, 9:76

Typo/grammar (Marc Eppley, 26 October 2009)

The final sentence of the paragraph following Table 2 beginning "We further investigated..." contains a grammatical error or typo. I'm not sure exactly what was intended.

"This suggests that the mutations in A/H1N1 that predispose for the human interaction pattern are remarkable of more prevalent than mutations that predispose for the swine interaction pattern." read full comment

Comment on: Veljkovic et al. BMC Structural Biology, 9:62