Is the GD Rose paper out?

John Kuszewski johnk at spasm.niddk.nih.gov
Wed Jul 12 13:24:20 EST 1995


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?

-- 
                                   _____________
                                   |        ___/_
                                   |        |/  /
                                   --  /\  //  /--
                                   ||  ||  /  /||
                                   ||  || /  / ||
                                   ||  ||/  /  ||
John Kuszewski                     ||  |/  /|  ||      
johnk at spasm.niddk.nih.gov          ||  /  /||  ||
                                   \/ /  / ||  \/
that's MISTER protein G to you!     |/__/|      |
                                      /_________|

"Biophysics has driven me to an attitude of apocalyptic doom"
   --Frank Delaglio



More information about the Proteins mailing list