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[交流] 【交流】AutoDock又出新工具“Vina”了！

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

经过实践证明，Vina比AutoDock的ADT工具先计算Grid，再进行Dock速度明显加快，值得一试！

[ Last edited by mingdong on 2009-9-13 at 18:56 ]

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