ADL: AutoDock Vina new beta release
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.
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
> 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,
> 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.
> Art Olson
> Arthur J. Olson, Ph.D.
> Department of Molecular Biology
> The Scripps Research Institute
> La Jolla, CA 92037
> tel. (858) 784-9702
> fax. (858) 784-2860
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