Rigid vs flexible docking comparison?
jeff at Adeno.wistar.upenn.edu
Wed Dec 20 10:26:42 EST 1995
In article <4av6tg$11r0 at pulp.ucs.ualberta.ca>,
max at mycroft.mmid.ualberta.ca (Max Cummings) writes:
>Is anyone aware of a comparison of rigid-body and
>flexible automated docking? Or a good review
>discussion of this?
>Max Cummings_____max at clouseau.mmid.ualberta.ca
I did a rigid vs. flexible study for the docking of two proteins from
the Adenovirus capsid. The results were quite dramatic and though I haven't
yet published them, I will be glad to share them with you.
Briefly, I used the Charmm molecular mechanics package to place the two
proteins and calculate an energy in a loop that explored the region of space
I was interested in. I then repeated the study with a minimization instead
of the simple energy sum.
The two methods gave results that differed by several angstroms. I
believe the minimization method does give superior results, however the trade
off is, of course, time.
I would be happy to discuss this further and show you some graphs of
the results I mentioned. If you (or anyone else) are interested reply via
The Wistar Institute
University of Pennsylvania
Jeff at aries.wistar.upenn.edu
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