[gmx-users] AutoDock --> GMX

Marc F. Lensink lensink at scmbb.ulb.ac.be
Wed Mar 2 11:08:48 CET 2005

On Wed, Mar 02, 2005 at 11:28:47AM +0200, Arturas wrote:
> Actually, docking followed by MD would be a very great tool.

for protein-protein docking, the use of MD is at the moment very
limited.  it's sometimes used for initial conformational scanning, and
also for side chain optimization, but although it's giving good
results, in the latter case it's outperformed by monte carlo and
rotamer scanning.  the strength of MD will probably be in a
combination with ED/PCA, since at the moment none of the
protein-protein docking methods seem to be able to handle
conformational changes very well.

Marc F. Lensink           http://www.biochem.oulu.fi/~lensink/
SCMBB, Université Libre de Bruxelles   lensink at scmbb.ulb.ac.be
Boulevard du Triomphe - CP 263, B-1050 Brussels, Belgium
tel: +32 2 650 5411  secr: +32 2 650 2013  fax: +32 2 650 5425

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