ADL: AutoDock Vina new beta release

reemelaby reemolaby at gmail.com
Sat Jun 6 23:04:05 PDT 2009


Dear Dr. Olson, 

         I am a new user to autodock and protein docking softwares in
general. I wanted to know how could i find the possible points in the
protein that ligands might bind to incase of not having ligands and i want
to design ones. 

Thank you, 
Reem


arthur olson wrote:
> 
> Dear AutoDock Users,
> 
> I want to alert AutoDock users to a new beta version of Vina, which is 
> now called AutoDock Vina, a new docking code developed by Oleg Trott in 
> my lab.  AutoDock Vena uses the same format for the ligand and receptor 
> files as AutoDock4, which can be prepared by AutoDock Tools, however its 
> input is much simpler, and there is no need to run AutoGrid before 
> runing the docking.  The scoring and optimization procedures in AutoDock 
> Vina are quite different than those in AutoDock4.
> 
> A paper announcing and describing AutoDock Vina is about to be submitted 
> for publicataion.  In the paper we compare its performance relative to 
> AutoDock4.  We have found AutoDock Vina is considerably faster than 
> AutoDock4, with comparable or better  docked structures for many
> complexes.
> 
> The newly released AutoDock Vina 1.0 beta 03 has the following changes 
> from the previous release:
> 
> (1) Improved estimation of the statistical influence of the
> flexibility of the ligand on its free energy of binding
> (2) Optimization of multiple interacting ligands is disabled
>  If you run Vina now with 0 or 2 or more ligands, you'll get an error,
> saying
> that this version requires exactly one ligand.
> 
> If people have a particular need to dock multiple ligands simultaneously,
> please let us know and we can discuss future possibilities.
> 
> AutoDock Vina 1.0 beta 03 is distributed as binary executables for both
> Linux and Windows platforms (sorry, no Mac OSX version yet).  It can be
> downloaded from vina.scripps.edu or via links from autodock.scripps.edu. 
> I encourage you to try the beta version and provide feedback to us.
> 
> Thanks,
> 
> Art Olson
> 
> 
> -- 
> @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
> 
> Arthur J. Olson, Ph.D.
> Professor
> Department of Molecular Biology
> The Scripps Research Institute
> La Jolla, CA 92037
> tel. (858) 784-9702 
> fax. (858) 784-2860
> http://www.scripps.edu/pub/olson-web
> 
> ________________________________________________
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> 
> 

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