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AutoDock, AutoLigand, MGLTools, Vina, PyRx and more.
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PostPosted: Wed Aug 12, 2009 3:22 pm 
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Joined: Wed Jun 24, 2009 2:28 am
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Hi

I am using vina for docking the small molecule and also try to use that for experimental. I able to repeat the known protein-small molecule
complex by vina and result is exactly replicating the experimental structures.

I do have question with respect to the ligand induced conformation changes in the protein upon binding, Is it any way we can achieve that using vina or other softwares combined with the vina. I am expecting changes not side chain overall loop or shifting of some secondary structures.


If any one has some experience, would be appreciate they can share that.

Thanks ,
venkat


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