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.
-----------------------------------------------------------------------
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 cus.cam.ac.uk | / \ \ fear where its been born"
-----------------------------------------------------------------------
WWW : http://nirvana.bioc.cam.ac.uk/~owde100/
-----------------------------------------------------------------------
