[Dock-fans] some questions about score methods, DelPhi and etc.

[Scott Brozell]

Hi,

On Wed, 11 Mar 2009, CAI Qixu wrote:

> I have several questions about DOCK 6.2:
>     1, there are so many score methods in DOCK. In common use, which one is
> better? The default grid-based energy score?

This reflects an underlying issue in docking.  In DOCKing, most scores
have advantages and disadvantages.  The default grid-based energy score
is still the workhorse since it is fast and decent.
Rescoring with more advanced scores, such as Amber score and PB/SA score,
has been used successfully.

See these for more details:
http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#Moustakasetal2006
http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#ShivakumaJMolBiol2008

>     2, Anyone know how to install DelPhi in fedora10? Or where to download
> DelPhi for fedora?

Not me;
this appears to be a current delphi site:
http://wiki.c2b2.columbia.edu/honiglab_public/index.php/Software:DelPhi

>     3, Is there any dock.in model for download in the website?

Yes, many in the tutorials for example:
http://dock.compbio.ucsf.edu/DOCK_6/tutorials/index.htm

Scott