HELP!!! Protein Graphics!!

Simon Brocklehurst Bioc smb18 at
Thu Jan 26 10:30:52 EST 1995

gerard at (Gerard Kleijwegt) writes:

>And how many experimental observations went into that molecular
>dynamics simulation ???  

   Quite a lot - ... the X-ray structure was used as input to
the program ;-)
And what was that about needing 80% identity to get a reasonable 
comparative model - is it my imagination, or is your estimate of the 
required sequence simliarity going up!

   For those that don't know, and aren't able to persuade a crystallographer
or NMR spectroscopist to solve the structure of their protein - there are 
NO examples of proteins more than 100 residue in length and that share 30% 
identity or more, that don't have essentially the same folds.  If you've 
got more than 50% identity, you probably won't even see too many shifts in 
structure of the core.  You can easily build "OK" models in these cases.

-- Simon
|  ,_ o     Simon M. Brocklehurst,
| /  //\,   Oxford Centre for Molecular Sciences
|   \>> |   Department of Biochemistry, University of Oxford,
|    \\,    Oxford, UK.
|           E-mail: smb at
|           WWW:

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