HELP!!! Protein Graphics!!

Orhan Ertughrul owde100 at bioc.cam.ac.uk
Thu Jan 26 05:49:44 EST 1995


In article <3g6k7d$13uk at columba.udac.uu.se>, gerard at rigel.bmc.uu.se (Gerard Kleijwegt) writes:
 > In article <3g5b3v$r68 at lyra.csx.cam.ac.uk>, owde100 at bioc.cam.ac.uk (Orhan Ertughrul) writes:
 > |> Remember though that it is only a model! Sometimes it's possible
 > |> to miss things even in crystal structures because the crystal 
 > |> latice may cause a protein to adopt a position that hides features.
 > |> Recently molecular dynamic work on a protein (I forget which one) 
 > |> revealed a channel to the active site that wasn't obvious from
 > |> the crystal structure for the previous reason. 
 > 
 > And how many experimental observations went into that molecular
 > dynamics simulation ???  If the answer is zero, I would bet that
 > the result of any such MD simulation is an artefact caused by the
 > particular combination of physical model + force field + algorithm
 > (+ random-number generator ? ;-) that is used.  At best it provides
 > a picture of something that may be physically possible, but without
 > any guarantee that it reflects biological reality.

Sure, but if anything this adds extra weight to the argument that
the results of computer simulations should be treated with caution.

Orhan.

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Orhan W.D. Ertughrul       |    /\         "It's hard enough to watch
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