In article <6g7n5o33bw.fsf at hodgkin.mbi.ucla.edu>, arne at hodgkin.mbi.ucla.edu (Arne Elofsson) (Arne Elofsson) writes:
|> > Yes, it's in the latest issue of Proteins as the lead article.
|> >
|>|> so what did you gues think. Is in time to try to join the AVP
|> beachvolleyboll teams, or should I continue my science carrier ?
Tee hee. I sometimes wonder whether or not I should get out
while the getting's good, too. I guess we're all suckers for
punishment.
|> 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
I think that part of this is explained by his having "solved" these
structures in short pieces (because the program is computationally
expensive).
But of course, you're right--the packing of secondary structure elements
isn't all that amazing. If you looked at the RMSDs of these models
to the crystal structures, they're pretty high--5 A is about the best
(if I'm remembering correctly), and some are 10 A away.
To start another thread, are models of that resolution useful for
anything?
|> It is interesting that such a simple method seems to work that well.
Precisely. I just saw Andrej Sali give a talk on MODELLER, and its
output is amazingly good. However, he's using a very large empirical
database. LINUS does extremely well for having so little starting
information.
|> 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
George Rose told us at his (now infamous?) NIH talk that it's more
like 1-2 weeks per "structure."
|> But atleast it gives me a few new ideas and I guess that makes
|> it a good paper. It is also described (more or less) good enough so
Yes.
One last question: Are there any other algorithms that predict
secondary structure as well as LINUS?
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John Kuszewski || |/ /| ||
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"Biophysics has driven me to an attitude of apocalyptic doom"
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