surface burial in energy calc's

Max Cummings max at mycroft.mmid.ualberta.ca
Tue Sep 20 16:12:14 EST 1994


Hi,

I sent this note to a couple of groups a few days ago
and thought maybe i should fish around in this one as well.
If you have responded to my request already thanks.


Lately I have been trying to review and summarize what people are doing
to approximate solvation effects in energy calculations. Our interest
is in molecular docking so we are looking for computationally cheap
approximations since ultimately we want to incorporate such a term
into the energy calculation which is used in our docking procedure.

Measuring the changes in buried/exposed surface areas of various atom
types (for eg. C, N/O, N+, O-, S) and multiplying the sums of these
changes by an "atomic solvation parameter" which converts these
areas into an energy contribution seems to be the commonly pursued
line. Indeed, I have done some analyses of the results obtained in
docking simulations which did not involve such a correction
in the energy calculations during the simulation and these
results indicate that such a correction will yield better
results in our docking simulations.

However...

There seems to be a variety of these correction parameters
floating around and I have not found a set of tests (published)
which really convinces me about the correctness of a
particular set of correction parameters. Also, there are surprisingly
few tests of these kinds of calculations published (see next
sentence). Online searches of such things as "solvation" or
"surface burial" yield either very few or way too many
references.

So...

If you are doing this kind of stuff, or even thinking about this,
let me know your opinion about approximate corrections for
solvation effects in molecular associations/protein folding.
Also, if you are aware of any significant references published
during the last 2 or 3 years (which do not have the names
eisenberg or honig on them - i have those!), especially
those discussing tests of such approximations, I would really
appreciate hearing about them.


--
Max Cummings_____max at clouseau.mmid.ualberta.ca




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