How to compare Protein folding success

Arne Elofsson arne at hodgkin.mbi.ucla.edu
Mon May 8 13:42:05 EST 1995


In article <950508105245.2020b39f at scri.fsu.edu> STRELETS at SCRI.FSU.EDU ("VICTOR B. STRELETS") writes:


> Almoust everybody in this area is talking about
> LOCAL folding first (and if GR slides sequence
> on 50aa segments first, he is doing local folding 
> too) and all fine and weird art next. What type
> of tests will be appropriate to test local folding
> algorithms? In this vase you don't have structure
> in whole, RMSD is inapplicable etc... Any idea?


An easy way would be to just count secondary structure 
prediction from these methods. If they really do better
than sec.str. predicition then it gets tougher to judge.

RMSD is bad, maybee contactmaps are better. Unfortunately
do I not know anything better than looking at the structures 
(or have a crystallographer to look at them).

arne


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               From: Arne Elofsson
         Email: arne at hodgkin.mbi.ucla.edu   			
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