From: Nicholas M Glykos (glykos_at_mbg.duth.gr)
Date: Mon Aug 30 2010 - 04:22:31 CDT
> is it necessary to clean water in between the protein? I understand we need
> to clean in channels or pores but is it required for globular proteins?
There is an interesting point to your question. Are (relatively large)
protein cavities empty or not ? If they contain (structurally disordered)
water molecules, then these waters will most probably not be visible in
electron density maps (and there will be no evidence for their presence
from the deposited PDB file). Last time (centuries ago) that we had this
issue (with a buried cavity of no less than 270 A^3 !), we ended-up doing
simulations both with and without waters in the cavity (not that this
ideal, the number of water molecules placed in the cavity will matter).
Still, if there time for just one simulation, I would rather remove any
waters 'trapped' in buried protein cavities.
-- Dr Nicholas M. Glykos, Department of Molecular Biology and Genetics, Democritus University of Thrace, University Campus, Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office) +302551030620, Ext.77620, Tel (lab) +302551030615, http://utopia.duth.gr/~glykos/
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