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.
This is a challenging problem and there are many programs that do this.
One review was published a few years ago: "Comparison of Nine Programs Predicting pKa Values of Pharmaceutical Substances", J. Chem. Inf. Model., 2009, 49 (12), pp 2801–2812
Surprisingly, the quantum program did poorly.
There's even a full book on the subject: Computational Approaches for the Prediction of pKa Values by George Shields and Paul Seybold. It covers both quantum and QSAR approaches.
Some of the best seem to be:
But there are dozens out there. I'd check the review articles and try a few.