You should also have a look at Privalov and Makhatadze's
papers last year (JMB 232. 639-659 and 660-779). There
is also another set of parameters from Murphy and Freire,
but I don't have the reference in front of me (some
help, Kip?) that appeared recently.
One major problem with comparing different solvation
parameters is that they model different thermodynamic
processes: eg., Murphy and Freire model the process of
moving from protein interior to exposed sites, but
Privalov and Makhatadze model the process of moving
from gas to solvated liquid. Thus, M&F's solvation
parameters include energies such as making/breaking
van der Waals contacts, which P&M's model treats
separately.
Another problem is that different groups do their
analysis with different atom "classes": Eisenberg
et al. lump all carbons together (if I'm remembering
correctly), but P&M treat aliphatic and aromatic
carbons separately.
Werner Braun et al. (JMB 233. 275-292, 1993) published
a paper that compares various solvation parameters
during torsion-angle-space energy minimization. Ooi's,
Eisenberg's, and Scheraga's parameter sets were among
those examined. None worked at all well, as the
gentleman from UCLA pointed out.
If you want to learn about solvation in general,
have a look at Ben-Naim's paper in Curr Op Struct
Biol 4. 264-268 (1994).
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John Kuszewski || |/ /| ||
johnk at spasm.niddk.nih.gov || / /|| ||
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that's MISTER protein G to you! |/__/| |
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