pKa

Each substance has a value called pKa which represents the pH at which the substance is 50% ionized.

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If the #G6HC=O substructure is present, then node2 applies, and the predicted value would be 3.6849957; if the substructure is absent, then node3 applies, and pKa 7.206913.

pKa prediction, or, how to convert a JCIM paper into Java Egon Willighagen 2008

Lee et al. published last week a paper on pKa prediction doi:10.1021/ci8001815.

Archive 2008-10-01 Egon Willighagen 2008

Lee et al. published last week a paper on pKa prediction doi:10.1021/ci8001815.

pKa prediction, or, how to convert a JCIM paper into Java Egon Willighagen 2008

Next, we need some logic to traverse the look up the predicted pKa from the decision tree, and I implemented this as:public static float predictIMolecule container throws CDKException

pKa prediction, or, how to convert a JCIM paper into Java Egon Willighagen 2008

As the paper says, the pKa, and in particular the ionic state of a molecule at physiological pH, affects pharmacokinetics and pharmacodynamics.

pKa prediction, or, how to convert a JCIM paper into Java Egon Willighagen 2008

Next, we need some logic to traverse the look up the predicted pKa from the decision tree, and I implemented this as:public static float predictIMolecule container throws CDKException

Archive 2008-10-01 Egon Willighagen 2008

If the #G6HC=O substructure is present, then node2 applies, and the predicted value would be 3.6849957; if the substructure is absent, then node3 applies, and pKa 7.206913.

Archive 2008-10-01 Egon Willighagen 2008

As the paper says, the pKa, and in particular the ionic state of a molecule at physiological pH, affects pharmacokinetics and pharmacodynamics.

Archive 2008-10-01 Egon Willighagen 2008

But ocean surface pH is about 8, and the pKa of bisulfate is 1.92, meaning that the bisulfate concentration in ocean waters is effectively zero.

Hansen and Schmidt: Predicting the Past? « Climate Audit 2006