Re: GB vs. GB/SA

From: David Case <>
Date: Tue 21 Nov 2000 10:15:42 -0800

On Mon, Nov 20, 2000, Andreas Svrcek-Seiler wrote:

> is there a significant difference between
> imlicit solvent MD trajecories with and without the SA contribution ?

For already compact proteins or nucleic acids, the differences between
GB and GB/SA in structural terms is generally small, in our (limited)
experience. There have been reports from France of narrower minor grooves
in DNA when using GB/SA (compared to GB alone), but we have not been
able to reproduce that here.

For larger conformational changes (e.g. protein/peptide folding), one might
expect larger differences, although this has not yet been tested. But I
wish to re-emphasize that our experience with GB/SA is rather limited so

...hope this helps...dac

David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |
Received on Tue Nov 21 2000 - 10:15:42 PST
Custom Search