I'd like to get a feel for what you folks think to be the "best" protocol
for structural refinement using NMR-based restraints, specifically for DNA
systems. How do in vacuo, implicit solvent, and explicit solvent methods
compare? How about conventional vs. time-averaged restraints? Restraints
based directly on NOE volumes vs. calculated upper/lower bounds (as with
MARDIGRAS)? How are your simulated annealing runs structured? How are
residual dipolar coupling restraints implemented for DNA?
I would appreciate any input you could provide. Citations would be very
helpful, as well. Thank you for your assistance.
.-. .-. .-. .-. .------------------------. .-. .-. .-. .-.
/|||X|||\ /|||X|||\ / Richard J. (Jake) Isaacs \ /|||X|||\ /|||X|||\
X|||/ \|||X|||/ \|||X Department of Molecular X|||/ \|||X|||/ \|||X
`-' `-' `-' `-' \ & Cellular Biochemistry / `-' `-' `-' `-'
.-. .-. .-. .-. / University of Kentucky \ .-. .-. .-. .-.
X|||\ /|||X|||\ /|||X 800 Rose St. X|||\ /|||X|||\ /|||X
\|||X|||/ \|||X|||/ \ Lexington, KY 40536-0084 / \|||X|||/ \|||X|||/
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Received on Tue May 14 2002 - 12:16:37 PDT
