Is the GD Rose paper out?

Arne Elofsson Arne Elofsson arne at hodgkin.mbi.ucla.edu
Wed Jul 12 17:52:06 EST 1995


In article <1995Jul12.182420.12069 at alw.nih.gov> johnk at spasm.niddk.nih.gov (John Kuszewski) writes:

> 
> In article <6g7n5o33bw.fsf at hodgkin.mbi.ucla.edu>, arne at hodgkin.mbi.ucla.edu (Arne Elofsson) (Arne Elofsson) writes:
> 
> 
> |> 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).
> 

or because it did not work for longer frags ?

> 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.
> 

5 A is very close to random for a compact 50 aa fragment with correct
sec.str. 10 A is  certainly random.

> To start another thread, are models of that resolution useful for
> anything?
> 

I think they could be usefull for searching a library of folds.
(Actually with 90% secondary prediction I'd bet you I can find 
the structure in a fold library given that it is not a new fold).

This is basically what Hubbard/Eddy and Benner did in Assilomar
but with much lower sec.str prediction accuracy.

> |> 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.
> 

Tell ous more. What is new in MODELLER. I did not know it did sec.str
predictions. 

Is Andrej at MSI nowadays ? (Making Modeller a commercial product ?)


> |> 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."  
> 
Even so, I'm sure they can borrow 10 workstations by someone
(mine for sure) and run 20 structures in a month.

> |> 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?
> 

The published record is (to my knowledge) is 72.2 % 
by Salamov & Solovyev


arne

--------------------------------------------------------
               From: Arne Elofsson
         Email: arne at hodgkin.mbi.ucla.edu   			
  WWW:  http://www.doe-mbi.ucla.edu/arne/main.html	



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