May
19
2011

A more dynamic literature review

Though I like posting them, and some of the readers like sifting through, the literature reviews always struck me as too static, I wanted to have a more nimble system that can allow readers to comment on a specific paper, to ‘like’ specific papers, and to be able to sort the list this way or another. Following the recent post on Annotator, it came to mind that Disqus might indeed be the answer for a few of these problems. So here is a pilot for this approach, let’s see how it goes. All the titles are posted as comments at the bottom, you can comment/ask questions on specific ones, show appreciation by ‘liking’ them, sort by popularity, moreover – you can add all the ones I missed!

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Written by Nir London in: Literature Reviews,Title Madness | Tags:

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  • http://dberkholz.com Donnie Berkholz

    For Fig 3b they say, “It is evident that the distribution of u03c4 is similar for each amino acid. There is no systematic dependence of either the mean value or standard deviation of u03c4 with respect to amino acid type.” I suspect that if they normalized the distributions to have equal areas under the curves, they’d discover that this is clearly not the case; the standard deviations vary quite a bit, although the means are indeed well-conserved.

  • http://cowsandmilk.net/ David Hall

    it would be nice if they would evaluate the CAPRI related to this….

  • http://rosettadesigngroup.com/blog Nir London

    It’s not in the public domain yet, but the results have been evaluated and reported to the participating groups. The manuscript is in the very final stages of preparations.

  • http://cowsandmilk.net/ David Hall

    I was meaning target 50 of round 24, which was predicting this complex, not the filtering/sorting round that is unpublished. I wouldn’t be surprised if everyone did well (considering logic can give you both sides of the complex, one side has mutated residues, and then you just put those residues where Ian Wilson’s antibody bound), but comparing our own predictions to 3r2x has made me curious about the performance of some other groups.

  • Alexandre Bonvin

    The scoring experiment should also be interesting…. We did sample the correct conformation, but also had other solutions in the head region that scored better in our hands (i.e. we did not limit ourselves to the “known” binding site).

  • http://rosettadesigngroup.com/blog Nir London

    That’s interesting, as they designed towards a very specific binding site but didn’t designed against any others – it’s like the achievement of specificity for ‘other’ binding partners – does high affinity implies specificity? many times it’s not the case.

  • http://www.facebook.com/iain.moal Iain Moal

    I suspect that most groups will have located the designed site. Irrespective, we found something close to 3r2x ranked #1. I presume that a binding site designed using an energy function is easy to locate using other energy functions, and that most people would have found the correct pose even without the information about which residues are mutated.

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