Is the GD Rose paper out?

David Jones jones at
Wed Jul 12 09:37:20 EST 1995

Arne Elofsson (arne at wrote:

> On the other side the packing of secondary structure elements is not that
> impressive. Looks pretty good for the fragments in fig 3 (1fb) and for
> 2 out of three 50 aa fragments of b562. but pcy, mbo and eglin does not 
> look that good (when you take into aspect that you have nearly perfect
> secondary structure prediction). MBO is not a very good test as apomyoglobin
> not is stable in water.

I think it would be accurate to say that there is _no_ secondary structure
packing beyond beta and alpha hairpins - and those interactions are given
on a plate. Clearly the current form of the method really makes no inroads
into tertiary structure prediction. However, the results in terms of
secondary structure prediction do appear good.

> It is interesting that such a simple method seems to work that well.

Yes, indeed.

> Unfortunately this is one of many studies that would be extremely
> much better if they had done some more rigourous testing, from 
> what I read in the John Hopkins journal, the run takes over night
> or so, which makes me wonder why they do not run this on 50 different
> proteins. I always get very very suspicious abot this method.
> How do I know that they did not try it on 50 proteins and it only worked
> in these 5 ? Probably not but they might have unintentionally have
> optimised things for this test set. Any study that do not contain
> a jack-knife test is much less impressive to me.

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