ADL: AutoDock Vina new beta release

Jian SUN sunjian.nku at gmail.com
Tue Jun 9 01:50:06 PDT 2009


hi, Dear Olson,

I watched your tutorial and found vina is really a powerful tool.
However, I still have some questions:

1) how many atom types can vina support?
2) would you please explain us a little more about the algorithm? As vina
dont generate grid file, how could it efficiently calculate the interaction?
When doing virutal screening, will vina still get better performance than
autodock4?

Thanks

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
> 
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
> 
> 

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