Protein structure from scratch?

Arne Elofsson arne at
Thu Aug 11 13:49:07 EST 1994

In article <32djkp$hbs at>, dopearso at (Douglas C Pearson) writes:
From: dopearso at (Douglas C Pearson)
Newsgroups: bionet.molec-model
Subject: Re: Protein structure from scratch?
Date: 11 Aug 1994 16:29:13 GMT
Organization: The Ohio State University
Lines: 23
Message-ID: <32djkp$hbs at>
References: <170097098S86.FJVAND00 at> <3287u5$7ki at charm.magnus.acs.o

>Floeckner Hannes <floeckn at> wrote:
>>I wonder what you mean with '65% accurate model'. This "percentage correct"
>>measure is, as far as I know, always used in connection with algorithms for
>>the prediction of secondary structure (like the EMBL prediction server, xy%
>>of the residues assigned the correct secondary structure). But these secondary
>>structure predictions don't give a 3D model of the protein.
Fred Cohen showed a long time ago that packing of a four helical boundle 

1. Presnell SR; Cohen FE.
     Topological distribution of four-alpha-helix bundles.
   Proceedings of the National Academy of Sciences of the United States of
   America, 1989 Sep, 86(17):6592-6.

and several other references

>>By the way, I don't think 65% is a good result.
Rost and sander showed that proteins are approximately 82% correct
(within a family) So it is not that bad.

>i believe the connection with secondary structure is correct (though i'd be 
>happy if somebody could confirm that for me...i'm just a second-year grad 
>student, for pete's sake!).  i agree, that's not the best model in the world,
>but if it's a choice between knowing something about a protein's secondary/
>tertiary structure and knowing nothing, what are you going to take?
>this type of modeling is good as a starting point.  nothing more.>

You really need to find a protein with some homology to get some idea
of the structure. Sec.Str itself is hardly good enough.


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