HELP!!! Protein Graphics!!

Orhan Ertughrul owde100 at
Thu Jan 26 05:49:44 EST 1995

In article <3g6k7d$13uk at>, gerard at (Gerard Kleijwegt) writes:
 > In article <3g5b3v$r68 at>, owde100 at (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 W.D. Ertughrul       |    /\         "It's hard enough to watch
University of Cambridge    |   /  \ /\      the news, let alone explain
Department of Biochemistry |  /    /  \     it to a child to cast its
Tennis Court Road          | /    /    \    eyes on nature over fields
Cambridge CB2 1QW          |/    /      \   of rape and corn, and tell
                           |  /\/        \  it without flinching not to
owde100 at      | /  \         \ fear where its been born"

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