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For docking calculations at different values of pH, I am working with flavonoids and would like to know about any software/server that can prepare ligands depending on the pH. Up to now I read about Maestro (Schrodinger) but it is too expensive for us. I wonder if you could suggest other alternatives.

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For this, you can try to use the LigpKa database server.

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Could you expand on your answer a bit to say why this would be a good choice, please? –  jonsca Feb 13 '13 at 3:21
    
Well, mainly, because it seems as if there is no big spectrum of available software for the task at hand. So it's a good suggestion in that it's maybe the only option. But I have no experience using it. –  TMOTTM Feb 13 '13 at 9:52
    
Understandable. It's just better to have some substance with the answer, as I don't know if you chose it because it has the best XYZ, the most reliable W, or because you like the splash screen. ;) Anyway, anything you know about it would be helpful to future readers of the question, is all. –  jonsca Feb 13 '13 at 22:55
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